0s autopkgtest [14:16:01]: starting date: 2024-03-12 0s autopkgtest [14:16:01]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [14:16:01]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7gb803pc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:perl,src:db5.3,src:gdbm,src:mmdebstrap --apt-upgrade bowtie2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=perl/5.38.2-3.2 db5.3/5.3.28+dfsg2-5 gdbm/1.23-5.1 mmdebstrap/1.4.3-6' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-ppc64el-7.secgroup --name adt-noble-ppc64el-bowtie2-20240312-141601-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 169s autopkgtest [14:18:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 169s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 170s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 170s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [450 kB] 170s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [40.9 kB] 170s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2783 kB] 171s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [598 kB] 172s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 172s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 172s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 172s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [3166 kB] 172s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 172s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [51.8 kB] 172s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 178s Fetched 7224 kB in 4s (1622 kB/s) 179s Reading package lists... 188s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s Calculating upgrade... 190s The following packages were automatically installed and are no longer required: 190s libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38 190s Use 'sudo apt autoremove' to remove them. 190s The following packages will be REMOVED: 190s dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl 190s The following NEW packages will be installed: 190s libgdbm-compat4t64 libgdbm6t64 190s The following packages have been kept back: 190s libperl5.38 190s The following packages will be upgraded: 190s firmware-sof-signed klibc-utils libklibc perl-base perl-modules-5.38 190s 5 upgraded, 2 newly installed, 5 to remove and 1 not upgraded. 190s Need to get 9154 kB of archives. 190s After this operation, 4149 kB disk space will be freed. 190s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-base ppc64el 5.38.2-3.2 [1916 kB] 190s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm6t64 ppc64el 1.23-5.1 [41.9 kB] 190s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm-compat4t64 ppc64el 1.23-5.1 [6972 B] 190s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 191s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el firmware-sof-signed all 2023.12.1-1ubuntu1 [3906 kB] 191s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el klibc-utils ppc64el 2.0.13-4 [120 kB] 191s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libklibc ppc64el 2.0.13-4 [53.7 kB] 192s Fetched 9154 kB in 1s (7445 kB/s) 192s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70101 files and directories currently installed.) 192s Removing dpkg-dev (1.22.4ubuntu5) ... 192s Removing libdpkg-perl (1.22.4ubuntu5) ... 192s Removing perl (5.38.2-3) ... 193s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69520 files and directories currently installed.) 193s Preparing to unpack .../perl-base_5.38.2-3.2_ppc64el.deb ... 193s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 193s Setting up perl-base (5.38.2-3.2) ... 194s dpkg: libgdbm6:ppc64el: dependency problems, but removing anyway as you requested: 194s python3-gdbm:ppc64el depends on libgdbm6 (>= 1.16). 194s man-db depends on libgdbm6 (>= 1.16). 194s libperl5.38:ppc64el depends on libgdbm6 (>= 1.21). 194s libgdbm-compat4:ppc64el depends on libgdbm6 (>= 1.16). 194s 194s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69520 files and directories currently installed.) 194s Removing libgdbm6:ppc64el (1.23-5) ... 194s Selecting previously unselected package libgdbm6t64:ppc64el. 194s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69515 files and directories currently installed.) 194s Preparing to unpack .../libgdbm6t64_1.23-5.1_ppc64el.deb ... 194s Unpacking libgdbm6t64:ppc64el (1.23-5.1) ... 194s dpkg: libgdbm-compat4:ppc64el: dependency problems, but removing anyway as you requested: 194s libperl5.38:ppc64el depends on libgdbm-compat4 (>= 1.18-3). 194s 194s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69521 files and directories currently installed.) 194s Removing libgdbm-compat4:ppc64el (1.23-5) ... 194s Selecting previously unselected package libgdbm-compat4t64:ppc64el. 194s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69516 files and directories currently installed.) 194s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_ppc64el.deb ... 194s Unpacking libgdbm-compat4t64:ppc64el (1.23-5.1) ... 194s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... 194s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 196s Preparing to unpack .../firmware-sof-signed_2023.12.1-1ubuntu1_all.deb ... 196s Unpacking firmware-sof-signed (2023.12.1-1ubuntu1) over (2.2.6-1ubuntu4) ... 196s Preparing to unpack .../klibc-utils_2.0.13-4_ppc64el.deb ... 196s Unpacking klibc-utils (2.0.13-4) over (2.0.13-2ubuntu1) ... 196s Preparing to unpack .../libklibc_2.0.13-4_ppc64el.deb ... 196s Unpacking libklibc:ppc64el (2.0.13-4) over (2.0.13-2ubuntu1) ... 196s Setting up libgdbm6t64:ppc64el (1.23-5.1) ... 196s Setting up libgdbm-compat4t64:ppc64el (1.23-5.1) ... 196s Setting up firmware-sof-signed (2023.12.1-1ubuntu1) ... 196s Setting up libklibc:ppc64el (2.0.13-4) ... 196s Setting up perl-modules-5.38 (5.38.2-3.2) ... 196s Setting up klibc-utils (2.0.13-4) ... 196s Processing triggers for libc-bin (2.39-0ubuntu2) ... 197s Processing triggers for man-db (2.12.0-3) ... 200s Processing triggers for initramfs-tools (0.142ubuntu20) ... 200s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 200s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 217s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 217s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 217s Reading package lists... 217s Building dependency tree... 217s Reading state information... 218s The following packages will be REMOVED: 218s libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* perl-modules-5.38* 218s 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded. 218s After this operation, 53.0 MB disk space will be freed. 218s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69533 files and directories currently installed.) 218s Removing libperl5.38:ppc64el (5.38.2-3) ... 219s Removing libgdbm-compat4t64:ppc64el (1.23-5.1) ... 219s Removing lto-disabled-list (47) ... 219s Removing make (4.3-4.1build1) ... 219s Removing perl-modules-5.38 (5.38.2-3.2) ... 219s Processing triggers for man-db (2.12.0-3) ... 220s Processing triggers for libc-bin (2.39-0ubuntu2) ... 222s sh: Attempting to set up Debian/Ubuntu apt sources automatically 222s sh: Distribution appears to be Ubuntu 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s eatmydata is already the newest version (131-1). 228s dbus is already the newest version (1.14.10-4ubuntu1). 228s dbus set to manually installed. 228s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 228s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 228s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 229s Reading package lists... 229s Building dependency tree... 229s Reading state information... 230s rng-tools-debian is already the newest version (2.4). 230s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 230s Reading package lists... 230s Building dependency tree... 230s Reading state information... 231s haveged is already the newest version (1.9.14-1ubuntu1). 231s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 231s Reading package lists... 231s Building dependency tree... 231s Reading state information... 231s The following additional packages will be installed: 231s libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list 231s make perl perl-modules-5.38 231s Suggested packages: 231s debian-keyring gcc | c-compiler git bzr make-doc perl-doc 231s libterm-readline-gnu-perl | libterm-readline-perl-perl 231s libtap-harness-archive-perl 231s Recommended packages: 231s build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl 231s libfile-fcntllock-perl 231s The following packages will be REMOVED: 232s libdb5.3 232s The following NEW packages will be installed: 232s dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 232s lto-disabled-list make perl perl-modules-5.38 232s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded. 232s Need to get 7626 kB/10.7 MB of archives. 232s After this operation, 57.2 MB of additional disk space will be used. 232s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdb5.3t64 ppc64el 5.3.28+dfsg2-5build1 [868 kB] 232s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libperl5.38t64 ppc64el 5.38.2-3.2 [4957 kB] 233s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl ppc64el 5.38.2-3.2 [231 kB] 233s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdpkg-perl all 1.22.4ubuntu5 [268 kB] 233s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el make ppc64el 4.3-4.1build1 [211 kB] 233s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el lto-disabled-list all 47 [12.4 kB] 233s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el dpkg-dev all 1.22.4ubuntu5 [1078 kB] 233s Fetched 7626 kB in 2s (4923 kB/s) 234s dpkg: libdb5.3:ppc64el: dependency problems, but removing anyway as you requested: 234s libsasl2-modules-db:ppc64el depends on libdb5.3. 234s libpython3.12-stdlib:ppc64el depends on libdb5.3. 234s libpython3.11-stdlib:ppc64el depends on libdb5.3. 234s libpam-modules:ppc64el depends on libdb5.3. 234s iproute2 depends on libdb5.3. 234s apt-utils depends on libdb5.3. 234s 234s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 67568 files and directories currently installed.) 234s Removing libdb5.3:ppc64el (5.3.28+dfsg2-4) ... 234s Selecting previously unselected package libdb5.3t64:ppc64el. 234s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 67562 files and directories currently installed.) 234s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5build1_ppc64el.deb ... 234s Unpacking libdb5.3t64:ppc64el (5.3.28+dfsg2-5build1) ... 234s Setting up libdb5.3t64:ppc64el (5.3.28+dfsg2-5build1) ... 234s Selecting previously unselected package perl-modules-5.38. 234s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 67568 files and directories currently installed.) 234s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... 234s Unpacking perl-modules-5.38 (5.38.2-3.2) ... 236s Selecting previously unselected package libgdbm-compat4t64:ppc64el. 236s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_ppc64el.deb ... 236s Unpacking libgdbm-compat4t64:ppc64el (1.23-5.1) ... 236s Selecting previously unselected package libperl5.38t64:ppc64el. 236s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_ppc64el.deb ... 236s Unpacking libperl5.38t64:ppc64el (5.38.2-3.2) ... 237s Selecting previously unselected package perl. 237s Preparing to unpack .../3-perl_5.38.2-3.2_ppc64el.deb ... 237s Unpacking perl (5.38.2-3.2) ... 237s Selecting previously unselected package libdpkg-perl. 237s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ... 237s Unpacking libdpkg-perl (1.22.4ubuntu5) ... 237s Selecting previously unselected package make. 237s Preparing to unpack .../5-make_4.3-4.1build1_ppc64el.deb ... 237s Unpacking make (4.3-4.1build1) ... 237s Selecting previously unselected package lto-disabled-list. 237s Preparing to unpack .../6-lto-disabled-list_47_all.deb ... 237s Unpacking lto-disabled-list (47) ... 238s Selecting previously unselected package dpkg-dev. 238s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ... 238s Unpacking dpkg-dev (1.22.4ubuntu5) ... 238s Setting up lto-disabled-list (47) ... 238s Setting up libgdbm-compat4t64:ppc64el (1.23-5.1) ... 238s Setting up make (4.3-4.1build1) ... 238s Setting up perl-modules-5.38 (5.38.2-3.2) ... 239s Setting up libperl5.38t64:ppc64el (5.38.2-3.2) ... 239s Setting up perl (5.38.2-3.2) ... 239s Setting up libdpkg-perl (1.22.4ubuntu5) ... 239s Setting up dpkg-dev (1.22.4ubuntu5) ... 239s Processing triggers for man-db (2.12.0-3) ... 241s Processing triggers for libc-bin (2.39-0ubuntu2) ... 241s Reading package lists... 241s Building dependency tree... 241s Reading state information... 242s The following packages will be REMOVED: 242s cloud-init* python3-configobj* python3-debconf* 242s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 242s After this operation, 3248 kB disk space will be freed. 243s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70114 files and directories currently installed.) 243s Removing cloud-init (24.1-0ubuntu1) ... 244s Removing python3-configobj (5.0.8-3) ... 244s Removing python3-debconf (1.5.86) ... 244s Processing triggers for man-db (2.12.0-3) ... 244s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69725 files and directories currently installed.) 244s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 246s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 246s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 246s Reading package lists... 247s Building dependency tree... 247s Reading state information... 247s linux-generic is already the newest version (6.8.0-11.11+1). 247s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 248s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 248s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 248s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 248s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 248s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 255s Reading package lists... 255s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 255s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 255s Reading package lists... 255s Building dependency tree... 255s Reading state information... 255s Calculating upgrade... 256s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 256s Reading package lists... 256s Building dependency tree... 256s Reading state information... 257s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 257s autopkgtest [14:20:18]: rebooting testbed after setup commands that affected boot 434s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 467s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 473s autopkgtest [14:23:54]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 474s autopkgtest [14:23:55]: testbed dpkg architecture: ppc64el 476s autopkgtest [14:23:57]: @@@@@@@@@@@@@@@@@@@@ apt-source bowtie2 477s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 477s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 477s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 480s Get:1 http://ftpmaster.internal/ubuntu noble/universe bowtie2 2.5.2-1 (dsc) [2513 B] 480s Get:2 http://ftpmaster.internal/ubuntu noble/universe bowtie2 2.5.2-1 (tar) [10.6 MB] 480s Get:3 http://ftpmaster.internal/ubuntu noble/universe bowtie2 2.5.2-1 (diff) [19.8 kB] 480s gpgv: Signature made Wed Jan 10 20:06:52 2024 UTC 480s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 480s gpgv: issuer "tillea@rki.de" 480s gpgv: Can't check signature: No public key 480s dpkg-source: warning: cannot verify inline signature for ./bowtie2_2.5.2-1.dsc: no acceptable signature found 481s autopkgtest [14:24:02]: testing package bowtie2 version 2.5.2-1 481s autopkgtest [14:24:02]: build not needed 492s autopkgtest [14:24:13]: test run-unit-test: preparing testbed 497s Reading package lists... 497s Building dependency tree... 497s Reading state information... 498s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 498s Starting 2 pkgProblemResolver with broken count: 0 498s Done 499s Done 499s Starting pkgProblemResolver with broken count: 0 499s Starting 2 pkgProblemResolver with broken count: 0 499s Done 500s The following additional packages will be installed: 500s bowtie2 bowtie2-examples libclone-perl libconfig-general-perl 500s libfile-which-perl libmath-random-perl libsys-info-base-perl 500s libsys-info-driver-linux-perl libsys-info-perl libtest-deep-perl 500s libunix-processors-perl 500s The following NEW packages will be installed: 500s bowtie2 bowtie2-examples libclone-perl libconfig-general-perl 500s libfile-which-perl libmath-random-perl libsys-info-base-perl 500s libsys-info-driver-linux-perl libsys-info-perl libtest-deep-perl 500s libunix-processors-perl 500s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 500s 1 not fully installed or removed. 500s Need to get 11.3 MB of archives. 500s After this operation, 15.1 MB of additional disk space will be used. 500s Get:1 http://ftpmaster.internal/ubuntu noble/universe ppc64el bowtie2 ppc64el 2.5.2-1 [1367 kB] 501s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el bowtie2-examples all 2.5.2-1 [9707 kB] 502s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libclone-perl ppc64el 0.46-1build1 [11.1 kB] 502s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libtest-deep-perl all 1.204-1 [47.1 kB] 502s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libfile-which-perl all 1.27-2 [12.5 kB] 502s Get:6 http://ftpmaster.internal/ubuntu noble/multiverse ppc64el libmath-random-perl ppc64el 0.72-2build3 [52.1 kB] 502s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsys-info-base-perl all 0.7807-4 [27.0 kB] 502s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libconfig-general-perl all 2.65-2 [57.1 kB] 502s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libunix-processors-perl ppc64el 2.046-3build2 [15.7 kB] 502s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsys-info-driver-linux-perl all 0.7905-6 [24.1 kB] 502s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsys-info-perl all 0.7811-3 [6662 B] 503s Fetched 11.3 MB in 2s (6783 kB/s) 503s Selecting previously unselected package bowtie2. 503s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69670 files and directories currently installed.) 503s Preparing to unpack .../00-bowtie2_2.5.2-1_ppc64el.deb ... 503s Unpacking bowtie2 (2.5.2-1) ... 503s Selecting previously unselected package bowtie2-examples. 503s Preparing to unpack .../01-bowtie2-examples_2.5.2-1_all.deb ... 503s Unpacking bowtie2-examples (2.5.2-1) ... 503s Selecting previously unselected package libclone-perl:ppc64el. 503s Preparing to unpack .../02-libclone-perl_0.46-1build1_ppc64el.deb ... 503s Unpacking libclone-perl:ppc64el (0.46-1build1) ... 503s Selecting previously unselected package libtest-deep-perl. 503s Preparing to unpack .../03-libtest-deep-perl_1.204-1_all.deb ... 503s Unpacking libtest-deep-perl (1.204-1) ... 503s Selecting previously unselected package libfile-which-perl. 503s Preparing to unpack .../04-libfile-which-perl_1.27-2_all.deb ... 503s Unpacking libfile-which-perl (1.27-2) ... 503s Selecting previously unselected package libmath-random-perl. 503s Preparing to unpack .../05-libmath-random-perl_0.72-2build3_ppc64el.deb ... 503s Unpacking libmath-random-perl (0.72-2build3) ... 503s Selecting previously unselected package libsys-info-base-perl. 503s Preparing to unpack .../06-libsys-info-base-perl_0.7807-4_all.deb ... 503s Unpacking libsys-info-base-perl (0.7807-4) ... 503s Selecting previously unselected package libconfig-general-perl. 503s Preparing to unpack .../07-libconfig-general-perl_2.65-2_all.deb ... 503s Unpacking libconfig-general-perl (2.65-2) ... 503s Selecting previously unselected package libunix-processors-perl:ppc64el. 503s Preparing to unpack .../08-libunix-processors-perl_2.046-3build2_ppc64el.deb ... 503s Unpacking libunix-processors-perl:ppc64el (2.046-3build2) ... 503s Selecting previously unselected package libsys-info-driver-linux-perl. 503s Preparing to unpack .../09-libsys-info-driver-linux-perl_0.7905-6_all.deb ... 503s Unpacking libsys-info-driver-linux-perl (0.7905-6) ... 503s Selecting previously unselected package libsys-info-perl. 503s Preparing to unpack .../10-libsys-info-perl_0.7811-3_all.deb ... 503s Unpacking libsys-info-perl (0.7811-3) ... 503s Setting up libfile-which-perl (1.27-2) ... 503s Setting up libconfig-general-perl (2.65-2) ... 503s Setting up libtest-deep-perl (1.204-1) ... 503s Setting up libmath-random-perl (0.72-2build3) ... 503s Setting up libclone-perl:ppc64el (0.46-1build1) ... 503s Setting up bowtie2 (2.5.2-1) ... 503s Setting up libunix-processors-perl:ppc64el (2.046-3build2) ... 503s Setting up bowtie2-examples (2.5.2-1) ... 503s Setting up libsys-info-base-perl (0.7807-4) ... 503s Setting up libsys-info-driver-linux-perl (0.7905-6) ... 503s Setting up libsys-info-perl (0.7811-3) ... 503s Setting up autopkgtest-satdep (0) ... 503s Processing triggers for man-db (2.12.0-3) ... 508s (Reading database ... 69930 files and directories currently installed.) 508s Removing autopkgtest-satdep (0) ... 509s autopkgtest [14:24:30]: test run-unit-test: [----------------------- 510s \1 better written as $1 at simple_tests.pl line 4674. 510s \1 better written as $1 at simple_tests.pl line 4675. 510s FASTA-continuous 1 (fw:1, sam:1) 510s References: 510s >0 510s AGCATCGATCAGTATCTGA 510s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 510s /usr/bin/bowtie2 -F 10,9 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz 510s @HD VN:1.5 SO:unsorted GO:query 510s @SQ SN:0 LN:19 510s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz" 510s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 510s seq1_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 510s FASTA-continuous 2 (fw:1, sam:1) 510s References: 510s >0 510s AGCATCGATCAGTATCTGA 510s /usr/bin/bowtie2 -F 10,9 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz 510s @HD VN:1.5 SO:unsorted GO:query 510s @SQ SN:0 LN:19 510s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz" 510s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 510s seq2_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 510s seq2_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 510s FASTA-continuous 3 (fw:1, sam:1) 510s References: 510s >0 510s AGCATCGATCAGTATCTGA 510s /usr/bin/bowtie2 -F 10,9 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp .simple_tests.gz 510s @HD VN:1.5 SO:unsorted GO:query 510s @SQ SN:0 LN:19 510s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp .simple_tests.gz" 510s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 510s FASTA-continuous 4 (fw:1, sam:1) 510s References: 510s >0 510s AGCATCGATCAGTATCTGA 510s /usr/bin/bowtie2 -F 10,9 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp .simple_tests.gz 511s @HD VN:1.5 SO:unsorted GO:query 511s @SQ SN:0 LN:19 511s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp .simple_tests.gz" 511s seq1_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 511s FASTA-continuous 5 (fw:1, sam:1) 511s References: 511s >0 511s AGCATCGATCAGTATCTGA 511s /usr/bin/bowtie2 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp .simple_tests.gz 511s @HD VN:1.5 SO:unsorted GO:query 511s @SQ SN:0 LN:19 511s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp .simple_tests.gz" 511s seq2_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 511s FASTA-continuous 6 (fw:1, sam:1) 511s References: 511s >0 511s AGCATCGATCAG 511s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 511s /usr/bin/bowtie2 -F 10,1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp .simple_tests.gz 511s @HD VN:1.5 SO:unsorted GO:query 511s @SQ SN:0 LN:12 511s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp .simple_tests.gz" 511s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 511s seq1_1 0 0 2 255 10M * 0 0 GCATCGATCA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 511s seq1_2 0 0 3 255 10M * 0 0 CATCGATCAG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 511s Align should not fail when first seq in ref is all Ns (fw:1, sam:1) 511s References: 511s >0 511s NNNNNNNNNNNNNNN 511s >1 511s AGCATCGATCAGTATCTGA 511s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 511s Warning: Encountered reference sequence with only gaps 511s Warning: Encountered reference sequence with only gaps 511s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG 511s @HD VN:1.5 SO:unsorted GO:query 511s @SQ SN:0 LN:15 511s @SQ SN:1 LN:19 511s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 511s 0 0 1 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 511s Align should not fail when multiple seqs are all Ns (fw:1, sam:1) 511s References: 511s >0 511s NNNNNNNNNNNNNNN 511s >1 511s NNNNNNNNNNNNNNN 511s >2 511s AGCATCGATCAGTATCTGA 511s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 511s Warning: Encountered reference sequence with only gaps 511s Warning: Encountered reference sequence with only gaps 511s Warning: Encountered reference sequence with only gaps 511s Warning: Encountered reference sequence with only gaps 511s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG 511s @HD VN:1.5 SO:unsorted GO:query 511s @SQ SN:0 LN:15 511s @SQ SN:1 LN:15 511s @SQ SN:2 LN:19 511s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 511s 0 0 2 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 511s Should account for stretch of Ns at beginning (fw:1, sam:1) 511s References: 511s >0 511s NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA 511s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 512s /usr/bin/bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG 512s @HD VN:1.5 SO:unsorted GO:query 512s @SQ SN:0 LN:34 512s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 512s 0 0 0 18 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 512s Cline 1 (fw:1, sam:1) 512s References: 512s >0 512s AGCATCGATCAGTATCTGA 512s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 512s /usr/bin/bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG 512s @HD VN:1.5 SO:unsorted GO:query 512s @SQ SN:0 LN:19 512s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 512s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 512s Cline 2 (fw:1, sam:1) 512s References: 512s >0 512s AGCATCGATCAGTATCTGA 512s /usr/bin/bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 512s @HD VN:1.5 SO:unsorted GO:query 512s @SQ SN:0 LN:19 512s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 512s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 512s Cline 2 (fw:1, sam:1) 512s References: 512s >0 512s AGCATCGATCAGTATCTGA 512s /usr/bin/bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP 512s @HD VN:1.5 SO:unsorted GO:query 512s @SQ SN:0 LN:19 512s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" 512s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG ABCDEDGHIJKLMNOP AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 512s Cline 4 (fw:1, sam:1) 512s References: 512s >0 512s AGCATCGATCAGTATCTGA 512s /usr/bin/bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO 512s Error: Read 0 has more read characters than quality values. 512s terminate called after throwing an instance of 'int' 514s Aborted (core dumped) 514s Cline 5 (fw:1, sam:1) 514s References: 514s >0 514s AGCATCGATCAGTATCTGA 514s /usr/bin/bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ 514s (ERR): bowtie2-align exited with value 134 514s Error: Read 0 has more quality values than read characters. 514s terminate called after throwing an instance of 'int' 514s Aborted (core dumped) 514s (ERR): bowtie2-align exited with value 134 514s trim-to: trim from 5'-end (fw:1, sam:1) 514s References: 514s >0 514s AGCATCGATCAGTATCTGA 514s /usr/bin/bowtie2 --trim-to 5:12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 514s 515s @HD VN:1.5 SO:unsorted GO:query 515s @SQ SN:0 LN:19 515s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 515s 0 0 0 7 255 12M * 0 0 GATCAGTATCTG IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 515s trim-to: trim from 3'-end (fw:1, sam:1) 515s References: 515s >0 515s AGCATCGATCAGTATCTGA 515s /usr/bin/bowtie2 --trim-to 3:12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 515s 515s @HD VN:1.5 SO:unsorted GO:query 515s @SQ SN:0 LN:19 515s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 515s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 515s trim-to: trim from 3'-end (default) (fw:1, sam:1) 515s References: 515s >0 515s AGCATCGATCAGTATCTGA 515s /usr/bin/bowtie2 --trim-to 12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 515s 515s @HD VN:1.5 SO:unsorted GO:query 515s @SQ SN:0 LN:19 515s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 515s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 515s trim-to: invalid position (fw:1, sam:1) 515s References: 515s >0 515s AGCATCGATCAGTATCTGA 515s /usr/bin/bowtie2 --trim-to 4:12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 515s 515s --trim-to: trim position must be either 3 or 5trim-to: invalid count (fw:1, sam:1) 515s References: 515s >0 515s AGCATCGATCAGTATCTGA 515s /usr/bin/bowtie2 --trim-to 5:-12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 515s 515s 515s Bowtie 2 version 2.5.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 515s Usage: 515s bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] 515s 515s Index filename prefix (minus trailing .X.bt2). 515s NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. 515s Files with #1 mates, paired with files in . 515s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 515s Files with #2 mates, paired with files in . 515s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 515s Files with unpaired reads. 515s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 515s Files with interleaved paired-end FASTQ/FASTA reads 515s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 515s Files are unaligned BAM sorted by read name. 515s File for SAM output (default: stdout) 515s 515s , , can be comma-separated lists (no whitespace) and can be 515s specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 515s 515s Options (defaults in parentheses): 515s 515s Input: 515s -q query input files are FASTQ .fq/.fastq (default) 515s --tab5 query input files are TAB5 .tab5 515s --tab6 query input files are TAB6 .tab6 515s --qseq query input files are in Illumina's qseq format 515s -f query input files are (multi-)FASTA .fa/.mfa 515s -r query input files are raw one-sequence-per-line 515s -F k:,i: query input files are continuous FASTA where reads 515s are substrings (k-mers) extracted from a FASTA file 515s and aligned at offsets 1, 1+i, 1+2i ... end of reference 515s -c , , are sequences themselves, not files 515s -s/--skip skip the first reads/pairs in the input (none) 515s -u/--upto stop after first reads/pairs (no limit) 515s -5/--trim5 trim bases from 5'/left end of reads (0) 515s -3/--trim3 trim bases from 3'/right end of reads (0) 515s --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end 515s If the read end is not specified then it defaults to 3 (0) 515s --phred33 qualities are Phred+33 (default) 515s --phred64 qualities are Phred+64 515s --int-quals qualities encoded as space-delimited integers 515s 515s Presets: Same as: 515s For --end-to-end: 515s --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 515s --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 515s --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default) 515s --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 515s 515s For --local: 515s --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 515s --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 515s --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) 515s --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 515s 515s Alignment: 515s -N max # mismatches in seed alignment; can be 0 or 1 (0) 515s -L length of seed substrings; must be >3, <32 (22) 515s -i interval between seed substrings w/r/t read len (S,1,1.15) 515s --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) 515s --dpad include extra ref chars on sides of DP table (15) 515s --gbar disallow gaps within nucs of read extremes (4) 515s --ignore-quals treat all quality values as 30 on Phred scale (off) 515s --nofw do not align forward (original) version of read (off) 515s --norc do not align reverse-complement version of read (off) 515s --no-1mm-upfront do not allow 1 mismatch alignments before attempting to 515s scan for the optimal seeded alignments 515s --end-to-end entire read must align; no clipping (on) 515s OR 515s --local local alignment; ends might be soft clipped (off) 515s 515s Scoring: 515s --ma match bonus (0 for --end-to-end, 2 for --local) 515s --mp max penalty for mismatch; lower qual = lower penalty (6) 515s --np penalty for non-A/C/G/Ts in read/ref (1) 515s --rdg , read gap open, extend penalties (5,3) 515s --rfg , reference gap open, extend penalties (5,3) 515s --score-min min acceptable alignment score w/r/t read length 515s (G,20,8 for local, L,-0.6,-0.6 for end-to-end) 515s 515s Reporting: 515s (default) look for multiple alignments, report best, with MAPQ 515s OR 515s -k report up to alns per read; MAPQ not meaningful 515s OR 515s -a/--all report all alignments; very slow, MAPQ not meaningful 515s 515s Effort: 515s -D give up extending after failed extends in a row (15) 515s -R for reads w/ repetitive seeds, try sets of seeds (2) 515s 515s Paired-end: 515s -I/--minins minimum fragment length (0) 515s -X/--maxins maximum fragment length (500) 515s --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) 515s --no-mixed suppress unpaired alignments for paired reads 515s --no-discordant suppress discordant alignments for paired reads 515s --dovetail concordant when mates extend past each other 515s --no-contain not concordant when one mate alignment contains other 515s --no-overlap not concordant when mates overlap at all 515s 515s BAM: 515s --align-paired-reads 515s Bowtie2 will, by default, attempt to align unpaired BAM reads. 515s Use this option to align paired-end reads instead. 515s --preserve-tags Preserve tags from the original BAM record by 515s appending them to the end of the corresponding SAM output. 515s 515s Output: 515s -t/--time print wall-clock time taken by search phases 515s --un write unpaired reads that didn't align to 515s --al write unpaired reads that aligned at least once to 515s --un-conc write pairs that didn't align concordantly to 515s --al-conc write pairs that aligned concordantly at least once to 515s (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. 515s --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) 515s --quiet print nothing to stderr except serious errors 515s --met-file send metrics to file at (off) 515s --met-stderr send metrics to stderr (off) 515s --met report internal counters & metrics every secs (1) 515s --no-unal suppress SAM records for unaligned reads 515s --no-head suppress header lines, i.e. lines starting with @ 515s --no-sq suppress @SQ header lines 515s --rg-id set read group id, reflected in @RG line and RG:Z: opt field 515s --rg add ("lab:value") to @RG line of SAM header. 515s Note: @RG line only printed when --rg-id is set. 515s --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments. 515s --sam-no-qname-trunc 515s Suppress standard behavior of truncating readname at first whitespace 515s at the expense of generating non-standard SAM. 515s --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record. 515s --soft-clipped-unmapped-tlen 515s Exclude soft-clipped bases when reporting TLEN 515s --sam-append-comment 515s Append FASTA/FASTQ comment to SAM record 515s 515s Performance: 515s -p/--threads number of alignment threads to launch (1) 515s --reorder force SAM output order to match order of input reads 515s --mm use memory-mapped I/O for index; many 'bowtie's can share 515s 515s Other: 515s --qc-filter filter out reads that are bad according to QSEQ filter 515s --seed seed for random number generator (0) 515s --non-deterministic 515s seed rand. gen. arbitrarily instead of using read attributes 515s --version print version information and quit 515s -h/--help print this usage message 515s Error: Encountered internal Bowtie 2 exception (#1) 515s Command: /usr/bin/bowtie2-align-s --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 515s (ERR): bowtie2-align exited with value 1 515s --trim-to: the number bases to trim must be at least 0 515s Bowtie 2 version 2.5.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 515s Usage: 515s bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] 515s 515s Index filename prefix (minus trailing .X.bt2). 515s NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. 515s Files with #1 mates, paired with files in . 515s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 515s Files with #2 mates, paired with files in . 515s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 515s Files with unpaired reads. 515s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 515s Files with interleaved paired-end FASTQ/FASTA reads 515s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 515s Files are unaligned BAM sorted by read name. 515s File for SAM output (default: stdout) 515s 515s , , can be comma-separated lists (no whitespace) and can be 515s specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 515s 515s Options (defaults in parentheses): 515s 515s Input: 515s -q query input files are FASTQ .fq/.fastq (default) 515s --tab5 query input files are TAB5 .tab5 515s --tab6 query input files are TAB6 .tab6 515s --qseq query input files are in Illumina's qseq format 515s -f query input files are (multi-)FASTA .fa/.mfa 515s -r query input files are raw one-sequence-per-line 515s -F k:,i: query input files are continuous FASTA where reads 515s are substrings (k-mers) extracted from a FASTA file 515s and aligned at offsets 1, 1+i, 1+2i ... end of reference 515s -c , , are sequences themselves, not files 515s -s/--skip skip the first reads/pairs in the input (none) 515s -u/--upto stop after first reads/pairs (no limit) 515s -5/--trim5 trim bases from 5'/left end of reads (0) 515s -3/--trim3 trim bases from 3'/right end of reads (0) 515s --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end 515s If the read end is not specified then it defaults to 3 (0) 515s --phred33 qualities are Phred+33 (default) 515s --phred64 qualities are Phred+64 515s --int-quals qualities encoded as space-delimited integers 515s 515s Presets: Same as: 515s For --end-to-end: 515s --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 515s --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 515s --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default) 515s --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 515s 515s For --local: 515s --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 515s --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 515s --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) 515s --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 515s 515s Alignment: 515s -N max # mismatches in seed alignment; can be 0 or 1 (0) 515s -L length of seed substrings; must be >3, <32 (22) 515s -i interval between seed substrings w/r/t read len (S,1,1.15) 515s --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) 515s --dpad include extra ref chars on sides of DP table (15) 515s --gbar disallow gaps within nucs of read extremes (4) 515s --ignore-quals treat all quality values as 30 on Phred scale (off) 515s --nofw do not align forward (original) version of read (off) 515s --norc do not align reverse-complement version of read (off) 515s --no-1mm-upfront do not allow 1 mismatch alignments before attempting to 515s scan for the optimal seeded alignments 515s --end-to-end entire read must align; no clipping (on) 515s OR 515s --local local alignment; ends might be soft clipped (off) 515s 515s Scoring: 515s --ma match bonus (0 for --end-to-end, 2 for --local) 515s --mp max penalty for mismatch; lower qual = lower penalty (6) 515s --np penalty for non-A/C/G/Ts in read/ref (1) 515s --rdg , read gap open, extend penalties (5,3) 515s --rfg , reference gap open, extend penalties (5,3) 515s --score-min min acceptable alignment score w/r/t read length 515s (G,20,8 for local, L,-0.6,-0.6 for end-to-end) 515s 515s Reporting: 515s (default) look for multiple alignments, report best, with MAPQ 515s OR 515s -k report up to alns per read; MAPQ not meaningful 515s OR 515s -a/--all report all alignments; very slow, MAPQ not meaningful 515s 515s Effort: 515s -D give up extending after failed extends in a row (15) 515s -R for reads w/ repetitive seeds, try sets of seeds (2) 515s 515s Paired-end: 515s -I/--minins minimum fragment length (0) 515s -X/--maxins maximum fragment length (500) 515s --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) 515s --no-mixed suppress unpaired alignments for paired reads 515s --no-discordant suppress discordant alignments for paired reads 515s --dovetail concordant when mates extend past each other 515s --no-contain not concordant when one mate alignment contains other 515s --no-overlap not concordant when mates overlap at all 515s 515s BAM: 515s --align-paired-reads 515s Bowtie2 will, by default, attempt to align unpaired BAM reads. 515s Use this option to align paired-end reads instead. 515s --preserve-tags Preserve tags from the original BAM record by 515s appending them to the end of the corresponding SAM output. 515s 515s Output: 515s -t/--time print wall-clock time taken by search phases 515s --un write unpaired reads that didn't align to 515s --al write unpaired reads that aligned at least once to 515s --un-conc write pairs that didn't align concordantly to 515s --al-conc write pairs that aligned concordantly at least once to 515s (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. 515s --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) 515s --quiet print nothing to stderr except serious errors 515s --met-file send metrics to file at (off) 515s --met-stderr send metrics to stderr (off) 515s --met report internal counters & metrics every secs (1) 515s --no-unal suppress SAM records for unaligned reads 515s --no-head suppress header lines, i.e. lines starting with @ 515s --no-sq suppress @SQ header lines 515s --rg-id set read group id, reflected in @RG line and RG:Z: opt field 515s --rg add ("lab:value") to @RG line of SAM header. 515s Note: @RG line only printed when --rg-id is set. 515s --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments. 515s --sam-no-qname-trunc 515s Suppress standard behavior of truncating readname at first whitespace 515s at the expense of generating non-standard SAM. 515s --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record. 515s --soft-clipped-unmapped-tlen 515s Exclude soft-clipped bases when reporting TLEN 515s --sam-append-comment 515s Append FASTA/FASTQ comment to SAM record 515s 515s Performance: 515s -p/--threads number of alignment threads to launch (1) 515s --reorder force SAM output order to match order of input reads 515s --mm use memory-mapped I/O for index; many 'bowtie's can share 515s 515s Other: 515s --qc-filter filter out reads that are bad according to QSEQ filter 515s --seed seed for random number generator (0) 515s --non-deterministic 515s seed rand. gen. arbitrarily instead of using read attributes 515s --version print version information and quit 515s -h/--help print this usage message 515s Error: Encountered internal Bowtie 2 exception (#1) 515s Command: /usr/bin/bowtie2-align-s --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 515s (ERR): bowtie2-align exited with value 1 515s Cline 7 (fw:1, sam:1) 515s References: 515s >0 515s AGCATCGATCAGTATCTGA 515s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 515s 515s @HD VN:1.5 SO:unsorted GO:query 515s @SQ SN:0 LN:19 515s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 515s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 515s Cline 8 (fw:1, sam:1) 515s References: 515s >0 515s AGCATCGATCAGTATCTGA 515s /usr/bin/bowtie2 --trim5 16 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 515s @HD VN:1.5 SO:unsorted GO:query 515s @SQ SN:0 LN:19 515s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 515s 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 515s Cline 9 (fw:1, sam:1) 515s References: 515s >0 515s AGCATCGATCAGTATCTGA 515s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 515s @HD VN:1.5 SO:unsorted GO:query 515s @SQ SN:0 LN:19 515s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 515s Cline multiread 1 (fw:1, sam:1) 515s References: 515s >0 515s AGCATCGATCAGTATCTGA 515s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII 515s 515s 515s @HD VN:1.5 SO:unsorted GO:query 515s @SQ SN:0 LN:19 515s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 515s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 515s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 515s Cline multiread 2 (fw:1, sam:1) 515s References: 515s >0 515s AGCATCGATCAGTATCTGA 515s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII 515s 515s 516s @HD VN:1.5 SO:unsorted GO:query 516s @SQ SN:0 LN:19 516s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 516s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 516s Cline multiread 3 (fw:1, sam:1) 516s References: 516s >0 516s AGCATCGATCAGTATCTGA 516s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG 516s 516s @HD VN:1.5 SO:unsorted GO:query 516s @SQ SN:0 LN:19 516s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" 516s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 516s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 516s Cline paired 1 (fw:1, sam:1) 516s References: 516s >0 516s AGCATCGATCAAAAACTGA 516s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 516s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII 516s @HD VN:1.5 SO:unsorted GO:query 516s @SQ SN:0 LN:19 516s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII" 516s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 516s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 516s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 516s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 516s Cline paired 2 (fw:1, sam:1) 516s References: 516s >0 516s AGCATCGATCAAAAACTGA 516s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII 516s @HD VN:1.5 SO:unsorted GO:query 516s @SQ SN:0 LN:19 516s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 516s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 516s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 516s Cline paired 3 (fw:1, sam:1) 516s References: 516s >0 516s AGCATCGATCAAAAACTGA 516s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII 516s @HD VN:1.5 SO:unsorted GO:query 516s @SQ SN:0 LN:19 516s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 516s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 516s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 516s Cline paired 4 (fw:1, sam:1) 516s References: 516s >0 516s AGCATCGATCAAAAACTGA 516s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII 517s @HD VN:1.5 SO:unsorted GO:query 517s @SQ SN:0 LN:19 517s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" 517s 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 517s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 517s Fastq 1 (fw:1, sam:1) 517s References: 517s >0 517s AGCATCGATCAGTATCTGA 517s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 517s /usr/bin/bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz 517s @HD VN:1.5 SO:unsorted GO:query 517s @SQ SN:0 LN:19 517s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz" 517s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 517s Fastq 2 (fw:1, sam:1) 517s References: 517s >0 517s AGCATCGATCAGTATCTGA 517s /usr/bin/bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz 517s @HD VN:1.5 SO:unsorted GO:query 517s @SQ SN:0 LN:19 517s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz" 517s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 517s Fastq 3 (fw:1, sam:1) 517s References: 517s >0 517s AGCATCGATCAGTATCTGA 517s /usr/bin/bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz 517s @HD VN:1.5 SO:unsorted GO:query 517s @SQ SN:0 LN:19 517s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" 517s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 517s Fastq 4 (fw:1, sam:1) 517s References: 517s >0 517s AGCATCGATCAGTATCTGA 517s /usr/bin/bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz 517s Error: Read r0 has more read characters than quality values. 517s terminate called after throwing an instance of 'int' 518s Aborted (core dumped) 518s (ERR): bowtie2-align exited with value 134 518s Fastq 5 (fw:1, sam:1) 518s References: 518s >0 518s AGCATCGATCAGTATCTGA 518s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz 518s Error: Read r0 has more read characters than quality values. 518s terminate called after throwing an instance of 'int' 518s Aborted (core dumped) 518s (ERR): bowtie2-align exited with value 134 518s Fastq 6 (fw:1, sam:1) 518s References: 518s >0 518s AGCATCGATCAGTATCTGA 518s /usr/bin/bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz 518s Error: reads file does not look like a FASTQ file 518s terminate called after throwing an instance of 'int' 518s Aborted (core dumped) 518s (ERR): bowtie2-align exited with value 134 518s Fastq 7 (fw:1, sam:1) 518s References: 518s >0 518s AGCATCGATCAGTATCTGA 518s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz 518s @HD VN:1.5 SO:unsorted GO:query 518s @SQ SN:0 LN:19 518s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz" 518s r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 518s Fastq 8 (fw:1, sam:1) 518s References: 518s >0 518s AGCATCGATCAGTATCTGA 518s /usr/bin/bowtie2 --trim5 16 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz 518s @HD VN:1.5 SO:unsorted GO:query 518s @SQ SN:0 LN:19 518s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" 518s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 518s Fastq 9 (fw:1, sam:1) 518s References: 518s >0 518s AGCATCGATCAGTATCTGA 518s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz 518s @HD VN:1.5 SO:unsorted GO:query 518s @SQ SN:0 LN:19 518s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz" 518s Fastq multiread 1 (fw:1, sam:1) 518s References: 518s >0 518s AGCATCGATCAGTATCTGA 518s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz 519s @HD VN:1.5 SO:unsorted GO:query 519s @SQ SN:0 LN:19 519s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz" 519s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 519s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 519s Fastq multiread 2 (fw:1, sam:1) 519s References: 519s >0 519s AGCATCGATCAGTATCTGA 519s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz 519s @HD VN:1.5 SO:unsorted GO:query 519s @SQ SN:0 LN:19 519s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz" 519s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 519s Fastq multiread 3 (fw:1, sam:1) 519s References: 519s >0 519s AGCATCGATCAGTATCTGA 519s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz 519s @HD VN:1.5 SO:unsorted GO:query 519s @SQ SN:0 LN:19 519s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz" 519s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 519s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 519s Fastq paired 1 (fw:1, sam:1) 519s References: 519s >0 519s AGCATCGATCAAAAACTGA 519s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 519s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 519s @HD VN:1.5 SO:unsorted GO:query 519s @SQ SN:0 LN:19 519s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 519s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 519s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 519s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 519s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 519s Fastq paired 2 (fw:1, sam:1) 519s References: 519s >0 519s AGCATCGATCAAAAACTGA 519s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 519s @HD VN:1.5 SO:unsorted GO:query 519s @SQ SN:0 LN:19 519s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 519s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 519s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 519s Fastq paired 3 (fw:1, sam:1) 519s References: 519s >0 519s AGCATCGATCAAAAACTGA 519s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 519s @HD VN:1.5 SO:unsorted GO:query 519s @SQ SN:0 LN:19 519s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 519s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 519s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 519s Fastq paired 4 (fw:1, sam:1) 519s References: 519s >0 519s AGCATCGATCAAAAACTGA 519s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 520s @HD VN:1.5 SO:unsorted GO:query 520s @SQ SN:0 LN:19 520s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 520s r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 520s r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 520s Fasta 1 (fw:1, sam:1) 520s References: 520s >0 520s AGCATCGATCAGTATCTGA 520s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 520s /usr/bin/bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz 520s @HD VN:1.5 SO:unsorted GO:query 520s @SQ SN:0 LN:19 520s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz" 520s r0 0 0 3 255 15M * 0 0 CATCGATCAGTATCT IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 520s Fasta 2 (fw:1, sam:1) 520s References: 520s >0 520s AGCATCGATCAGTATCTGA 520s /usr/bin/bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz 520s @HD VN:1.5 SO:unsorted GO:query 520s @SQ SN:0 LN:19 520s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" 520s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 520s Fasta 3 (fw:1, sam:1) 520s References: 520s >0 520s AGCATCGATCAGTATCTGA 520s /usr/bin/bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz 520s @HD VN:1.5 SO:unsorted GO:query 520s @SQ SN:0 LN:19 520s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz" 520s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 520s Fasta 5 (fw:1, sam:1) 520s References: 520s >0 520s AGCATCGATCAGTATCTGA 520s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz 520s Error: reads file does not look like a FASTA file 520s terminate called after throwing an instance of 'int' 520s Aborted (core dumped) 520s (ERR): bowtie2-align exited with value 134 520s Fasta 6 (fw:1, sam:1) 520s References: 520s >0 520s AGCATCGATCAGTATCTGA 520s /usr/bin/bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz 521s Error: reads file does not look like a FASTA file 521s terminate called after throwing an instance of 'int' 521s Aborted (core dumped) 521s (ERR): bowtie2-align exited with value 134 521s Fasta 7 (fw:1, sam:1) 521s References: 521s >0 521s AGCATCGATCAGTATCTGA 521s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz 521s @HD VN:1.5 SO:unsorted GO:query 521s @SQ SN:0 LN:19 521s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz" 521s r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 521s Fasta 8 (fw:1, sam:1) 521s References: 521s >0 521s AGCATCGATCAGTATCTGA 521s /usr/bin/bowtie2 --trim3 16 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz 521s @HD VN:1.5 SO:unsorted GO:query 521s @SQ SN:0 LN:19 521s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz" 521s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 521s Fasta 9 (fw:1, sam:1) 521s References: 521s >0 521s AGCATCGATCAGTATCTGA 521s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz 521s @HD VN:1.5 SO:unsorted GO:query 521s @SQ SN:0 LN:19 521s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" 521s Fasta multiread 1 (fw:1, sam:1) 521s References: 521s >0 521s AGCATCGATCAGTATCTGA 521s /usr/bin/bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz 521s @HD VN:1.5 SO:unsorted GO:query 521s @SQ SN:0 LN:19 521s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz" 521s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 521s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 521s Fasta multiread 2 (fw:1, sam:1) 521s References: 521s >0 521s AGCATCGATCAGTATCTGA 521s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz 522s @HD VN:1.5 SO:unsorted GO:query 522s @SQ SN:0 LN:19 522s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz" 522s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 522s Fasta multiread 3 (fw:1, sam:1) 522s References: 522s >0 522s AGCATCGATCAGTATCTGA 522s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz 522s @HD VN:1.5 SO:unsorted GO:query 522s @SQ SN:0 LN:19 522s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz" 522s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 522s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 522s Fasta multiline 1 (fw:1, sam:1) 522s References: 522s >0 522s AGCATCGATCAGTATCTGA 522s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz 522s @HD VN:1.5 SO:unsorted GO:query 522s @SQ SN:0 LN:19 522s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz" 522s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 522s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 522s Fasta multiline 2 (fw:1, sam:1) 522s References: 522s >0 522s AGCATCGATCAGTATCTGA 522s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz 522s @HD VN:1.5 SO:unsorted GO:query 522s @SQ SN:0 LN:19 522s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz" 522s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 522s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 522s Fasta multiline 3 (fw:1, sam:1) 522s References: 522s >0 522s AGCATCGATCAGTATCTGA 522s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz 522s @HD VN:1.5 SO:unsorted GO:query 522s @SQ SN:0 LN:19 522s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz" 522s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 522s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 522s Fasta paired 1 (fw:1, sam:1) 522s References: 522s >0 522s AGCATCGATCAAAAACTGA 522s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 523s /usr/bin/bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 523s @HD VN:1.5 SO:unsorted GO:query 523s @SQ SN:0 LN:19 523s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 523s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 523s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 523s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 523s r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP 523s Fasta paired 2 (fw:1, sam:1) 523s References: 523s >0 523s AGCATCGATCAAAAACTGA 523s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 523s @HD VN:1.5 SO:unsorted GO:query 523s @SQ SN:0 LN:19 523s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 523s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 523s r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP 523s Fasta paired 3 (fw:1, sam:1) 523s References: 523s >0 523s AGCATCGATCAAAAACTGA 523s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 523s @HD VN:1.5 SO:unsorted GO:query 523s @SQ SN:0 LN:19 523s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 523s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 523s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 523s Fasta paired 4 (fw:1, sam:1) 523s References: 523s >0 523s AGCATCGATCAAAAACTGA 523s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 523s @HD VN:1.5 SO:unsorted GO:query 523s @SQ SN:0 LN:19 523s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 523s 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 523s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 523s Raw 1 (fw:1, sam:1) 523s References: 523s >0 523s AGCATCGATCAGTATCTGA 523s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 523s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz 523s @HD VN:1.5 SO:unsorted GO:query 523s @SQ SN:0 LN:19 523s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz" 523s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 523s Raw 2 (fw:1, sam:1) 523s References: 523s >0 523s AGCATCGATCAGTATCTGA 523s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz 524s @HD VN:1.5 SO:unsorted GO:query 524s @SQ SN:0 LN:19 524s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz" 524s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 524s Raw 3 (fw:1, sam:1) 524s References: 524s >0 524s AGCATCGATCAGTATCTGA 524s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz 524s @HD VN:1.5 SO:unsorted GO:query 524s @SQ SN:0 LN:19 524s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz" 524s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 524s Raw 7 (fw:1, sam:1) 524s References: 524s >0 524s AGCATCGATCAGTATCTGA 524s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz 524s @HD VN:1.5 SO:unsorted GO:query 524s @SQ SN:0 LN:19 524s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz" 524s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 524s Raw 8 (fw:1, sam:1) 524s References: 524s >0 524s AGCATCGATCAGTATCTGA 524s /usr/bin/bowtie2 --trim3 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz 524s @HD VN:1.5 SO:unsorted GO:query 524s @SQ SN:0 LN:19 524s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz" 524s 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 524s Raw 9 (fw:1, sam:1) 524s References: 524s >0 524s AGCATCGATCAGTATCTGA 524s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz 524s @HD VN:1.5 SO:unsorted GO:query 524s @SQ SN:0 LN:19 524s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz" 524s Raw multiread 1 (fw:1, sam:1) 524s References: 524s >0 524s AGCATCGATCAGTATCTGA 524s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz 524s @HD VN:1.5 SO:unsorted GO:query 524s @SQ SN:0 LN:19 524s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz" 524s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 524s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 524s Raw multiread 2 (fw:1, sam:1) 524s References: 524s >0 524s AGCATCGATCAGTATCTGA 524s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz 524s @HD VN:1.5 SO:unsorted GO:query 524s @SQ SN:0 LN:19 524s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz" 524s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 524s Raw multiread 3 (fw:1, sam:1) 524s References: 524s >0 524s AGCATCGATCAGTATCTGA 524s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz 524s @HD VN:1.5 SO:unsorted GO:query 524s @SQ SN:0 LN:19 524s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" 524s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 524s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 524s Raw paired 1 (fw:1, sam:1) 524s References: 524s >0 524s AGCATCGATCAAAAACTGA 524s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 525s /usr/bin/bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 525s @HD VN:1.5 SO:unsorted GO:query 525s @SQ SN:0 LN:19 525s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 525s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 525s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 525s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 525s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 525s Raw paired 2 (fw:1, sam:1) 525s References: 525s >0 525s AGCATCGATCAAAAACTGA 525s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 525s @HD VN:1.5 SO:unsorted GO:query 525s @SQ SN:0 LN:19 525s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 525s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 525s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 525s Raw paired 3 (fw:1, sam:1) 525s References: 525s >0 525s AGCATCGATCAAAAACTGA 525s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 525s @HD VN:1.5 SO:unsorted GO:query 525s @SQ SN:0 LN:19 525s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 525s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 525s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 525s Raw paired 4 (fw:1, sam:1) 525s References: 525s >0 525s AGCATCGATCAAAAACTGA 525s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 525s @HD VN:1.5 SO:unsorted GO:query 525s @SQ SN:0 LN:19 525s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 525s 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 525s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 525s Tabbed 1 (fw:1, sam:1) 525s References: 525s >0 525s AGCATCGATCAGTATCTGA 525s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 525s /usr/bin/bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 525s @HD VN:1.5 SO:unsorted GO:query 525s @SQ SN:0 LN:19 525s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 525s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 525s Tabbed 2 (fw:1, sam:1) 525s References: 525s >0 525s AGCATCGATCAGTATCTGA 525s /usr/bin/bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 525s @HD VN:1.5 SO:unsorted GO:query 525s @SQ SN:0 LN:19 525s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 525s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 525s Tabbed 3 (fw:1, sam:1) 525s References: 525s >0 525s AGCATCGATCAGTATCTGA 525s /usr/bin/bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 526s @HD VN:1.5 SO:unsorted GO:query 526s @SQ SN:0 LN:19 526s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 526s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 526s Tabbed 4 (fw:1, sam:1) 526s References: 526s >0 526s AGCATCGATCAGTATCTGA 526s /usr/bin/bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 526s Error: Read r0 has more read characters than quality values. 526s terminate called after throwing an instance of 'int' 526s Aborted (core dumped) 526s (ERR): bowtie2-align exited with value 134 526s Tabbed 5 (fw:1, sam:1) 526s References: 526s >0 526s AGCATCGATCAGTATCTGA 526s /usr/bin/bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 526s Error: Read r0 has more quality values than read characters. 526s terminate called after throwing an instance of 'int' 526s Aborted (core dumped) 526s (ERR): bowtie2-align exited with value 134 526s Tabbed 7 (fw:1, sam:1) 526s References: 526s >0 526s AGCATCGATCAGTATCTGA 526s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 526s @HD VN:1.5 SO:unsorted GO:query 526s @SQ SN:0 LN:19 526s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 526s r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 526s Tabbed 8 (fw:1, sam:1) 526s References: 526s >0 526s AGCATCGATCAGTATCTGA 526s /usr/bin/bowtie2 --trim5 16 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 526s @HD VN:1.5 SO:unsorted GO:query 526s @SQ SN:0 LN:19 526s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 526s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 526s Tabbed 9 (fw:1, sam:1) 526s References: 526s >0 526s AGCATCGATCAGTATCTGA 526s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 526s @HD VN:1.5 SO:unsorted GO:query 526s @SQ SN:0 LN:19 526s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 526s Tabbed multiread 1 (fw:1, sam:1) 526s References: 526s >0 526s AGCATCGATCAGTATCTGA 526s /usr/bin/bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 527s @HD VN:1.5 SO:unsorted GO:query 527s @SQ SN:0 LN:19 527s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 527s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 527s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 527s Tabbed multiread 2 (fw:1, sam:1) 527s References: 527s >0 527s AGCATCGATCAGTATCTGA 527s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 527s @HD VN:1.5 SO:unsorted GO:query 527s @SQ SN:0 LN:19 527s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 527s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 527s Tabbed multiread 3 (fw:1, sam:1) 527s References: 527s >0 527s AGCATCGATCAGTATCTGA 527s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 527s @HD VN:1.5 SO:unsorted GO:query 527s @SQ SN:0 LN:19 527s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 527s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 527s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 527s Tabbed paired 1 (fw:1, sam:1) 527s References: 527s >0 527s AGCATCGATCAAAAACTGA 527s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 527s /usr/bin/bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 527s @HD VN:1.5 SO:unsorted GO:query 527s @SQ SN:0 LN:19 527s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 527s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 527s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 527s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 527s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 527s Tabbed paired 2 (fw:1, sam:1) 527s References: 527s >0 527s AGCATCGATCAAAAACTGA 527s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 527s @HD VN:1.5 SO:unsorted GO:query 527s @SQ SN:0 LN:19 527s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 527s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 527s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 527s Tabbed paired 3 (fw:1, sam:1) 527s References: 527s >0 527s AGCATCGATCAAAAACTGA 527s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 528s @HD VN:1.5 SO:unsorted GO:query 528s @SQ SN:0 LN:19 528s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 528s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 528s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 528s Tabbed paired 4 (fw:1, sam:1) 528s References: 528s >0 528s AGCATCGATCAAAAACTGA 528s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 528s @HD VN:1.5 SO:unsorted GO:query 528s @SQ SN:0 LN:19 528s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 528s r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 528s r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 528s Qseq 1 (fw:1, sam:1) 528s References: 528s >0 528s AGCATCGATCAGTATCTGA 528s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 528s /usr/bin/bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 528s @HD VN:1.5 SO:unsorted GO:query 528s @SQ SN:0 LN:19 528s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 528s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 528s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 528s Qseq 2 (fw:1, sam:1) 528s References: 528s >0 528s AGCATCGATCAGTATCTGA 528s /usr/bin/bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 528s @HD VN:1.5 SO:unsorted GO:query 528s @SQ SN:0 LN:19 528s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 528s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 528s Qseq 3 (fw:1, sam:1) 528s References: 528s >0 528s AGCATCGATCAGTATCTGA 528s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 528s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 528s @HD VN:1.5 SO:unsorted GO:query 528s @SQ SN:0 LN:19 528s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 528s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 528s Qseq 4 (fw:1, sam:1) 528s References: 528s >0 528s AGCATCGATCAGTATCTGA 528s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 528s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 528s Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values. 528s terminate called after throwing an instance of 'int' 529s Aborted (core dumped) 529s (ERR): bowtie2-align exited with value 134 529s Qseq 7 (fw:1, sam:1) 529s References: 529s >0 529s AGCATCGATCAGTATCTGA 529s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 529s @HD VN:1.5 SO:unsorted GO:query 529s @SQ SN:0 LN:19 529s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 529s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 529s Qseq 8 (fw:1, sam:1) 529s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 529s References: 529s >0 529s AGCATCGATCAGTATCTGA 529s /usr/bin/bowtie2 --trim3 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 529s @HD VN:1.5 SO:unsorted GO:query 529s @SQ SN:0 LN:19 529s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 529s MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 529s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 529s Qseq 9 (fw:1, sam:1) 529s References: 529s >0 529s AGCATCGATCAGTATCTGA 529s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 529s @HD VN:1.5 SO:unsorted GO:query 529s @SQ SN:0 LN:19 529s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 529s Qseq multiread 1 (fw:1, sam:1) 529s References: 529s >0 529s AGCATCGATCAGTATCTGA 529s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 529s @HD VN:1.5 SO:unsorted GO:query 529s @SQ SN:0 LN:19 529s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 529s MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 529s MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 529s Qseq multiread 2 (fw:1, sam:1) 529s References: 529s >0 529s AGCATCGATCAGTATCTGA 529s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 529s @HD VN:1.5 SO:unsorted GO:query 529s @SQ SN:0 LN:19 529s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 529s MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 529s Qseq multiread 3 (fw:1, sam:1) 529s References: 529s >0 529s AGCATCGATCAGTATCTGA 529s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 530s @HD VN:1.5 SO:unsorted GO:query 530s @SQ SN:0 LN:19 530s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 530s MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 530s MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 530s Qseq paired 1 (fw:1, sam:1) 530s References: 530s >0 530s AGCATCGATCAAAAACTGA 530s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 530s /usr/bin/bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz 530s @HD VN:1.5 SO:unsorted GO:query 530s @SQ SN:0 LN:19 530s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" 530s MachName_RunNum_Lane_Tile_10_10_Index 99 0 1 255 10M = 9 19 AGCATCGATC ABCBGACBCB AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 530s MachName_RunNum_Lane_Tile_10_10_Index 147 0 9 255 11M = 1 -19 TCAAAAACTGA ABCBCAGBCBA AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 530s MachName_RunNum_Lane_Tile_12_15_Index 83 0 9 255 11M = 1 -19 TCAAAAACTGA 57865494859 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 530s MachName_RunNum_Lane_Tile_12_15_Index 163 0 1 255 10M = 9 19 AGCATCGATC AGGCBBGCBG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 530s Qseq paired 2 (fw:1, sam:1) 530s References: 530s >0 530s AGCATCGATCAAAAACTGA 530s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz 530s @HD VN:1.5 SO:unsorted GO:query 530s @SQ SN:0 LN:19 530s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" 530s MachName_RunNum_Lane_Tile_12_15_Index 83 0 9 255 11M = 1 -19 TCAAAAACTGA 57865494859 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 530s MachName_RunNum_Lane_Tile_12_15_Index 163 0 1 255 10M = 9 19 AGCATCGATC AGGCBBGCBG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 530s Left-align insertion (fw:1, sam:1) 530s References: 530s >0 530s GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 530s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 530s /usr/bin/bowtie2 --quiet --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 530s @HD VN:1.5 SO:unsorted GO:query 530s @SQ SN:0 LN:73 530s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 530s r0 0 0 23 24 2M1I40M * 0 0 ACAAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:42 YT:Z:UU 530s Left-align deletion (fw:1, sam:1) 530s References: 530s >0 530s GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 530s /usr/bin/bowtie2 --quiet --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 530s @HD VN:1.5 SO:unsorted GO:query 530s @SQ SN:0 LN:73 530s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 530s r0 0 0 19 40 6M1D39M * 0 0 ACGTACAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^A39 YT:Z:UU 530s Left-align insertion with mismatch at LHS (fw:1, sam:1) 530s References: 530s >0 530s GCGATATCTACGACTGCTACGCCCAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 530s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 530s /usr/bin/bowtie2 --quiet --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 531s @HD VN:1.5 SO:unsorted GO:query 531s @SQ SN:0 LN:73 531s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 531s r0 0 0 5 24 20M1D45M * 0 0 TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:20^A0A44 YT:Z:UU 531s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 531s References: 531s >0 531s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG 531s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 531s /usr/bin/bowtie2 --fr --quiet --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 531s @HD VN:1.5 SO:unsorted GO:query 531s @SQ SN:0 LN:1192 531s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 531s r0 65 0 3 42 38M = 1148 0 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UP 531s r0 129 0 1148 1 42M = 3 0 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YT:Z:UP 531s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 531s References: 531s >0 531s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG 531s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 531s /usr/bin/bowtie2 --fr --quiet --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 531s @HD VN:1.5 SO:unsorted GO:query 531s @SQ SN:0 LN:1028 531s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 531s r0 65 0 3 42 38M = 982 1021 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:DP 531s r0 129 0 982 42 42M = 3 -1021 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:DP 531s MREVERSE flag is set if mate does not align (fw:1, sam:1) 531s References: 531s >0 531s TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG 531s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 532s /usr/bin/bowtie2 --fr --quiet --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 532s @HD VN:1.5 SO:unsorted GO:query 532s @SQ SN:0 LN:250 532s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 532s r0 89 0 51 42 100M = 51 0 TTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UP 532s r0 165 0 51 0 * = 51 0 CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 532s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 532s References: 532s >0 532s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG 532s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 532s /usr/bin/bowtie2 --fr --quiet --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 532s @HD VN:1.5 SO:unsorted GO:query 532s @SQ SN:0 LN:290 532s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 532s r0 99 0 3 1 38M = 246 285 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:CP 532s r0 147 0 246 1 42M = 3 -285 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:CP 532s MD:Z 1 (fw:1, sam:1) 532s References: 532s >0 532s CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 532s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 532s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 532s @HD VN:1.5 SO:unsorted GO:query 532s @SQ SN:0 LN:54 532s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 532s r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU 532s MD:Z 1 (fw:0, sam:1) 532s References: 532s >0 532s CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 532s /usr/bin/bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 532s @HD VN:1.5 SO:unsorted GO:query 532s @SQ SN:0 LN:54 532s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 532s r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU 532s MD:Z 2 (fw:1, sam:1) 532s References: 532s >0 532s CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 532s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 533s /usr/bin/bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 533s @HD VN:1.5 SO:unsorted GO:query 533s @SQ SN:0 LN:54 533s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 533s r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU 533s MD:Z 2 (fw:0, sam:1) 533s References: 533s >0 533s CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 533s /usr/bin/bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 533s @HD VN:1.5 SO:unsorted GO:query 533s @SQ SN:0 LN:54 533s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 533s r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU 533s MD:Z 3 (fw:1, sam:1) 533s References: 533s >0 533s CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 533s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 533s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 533s @HD VN:1.5 SO:unsorted GO:query 533s @SQ SN:0 LN:55 533s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 533s r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU 533s MD:Z 3 (fw:0, sam:1) 533s References: 533s >0 533s CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 533s /usr/bin/bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 533s @HD VN:1.5 SO:unsorted GO:query 533s @SQ SN:0 LN:55 533s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 533s r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU 533s MD:Z 4 (fw:1, sam:1) 533s References: 533s >0 533s CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 533s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 533s /usr/bin/bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 534s @HD VN:1.5 SO:unsorted GO:query 534s @SQ SN:0 LN:55 534s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 534s r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:3 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^NN0N39 YT:Z:UU 534s MD:Z 4 (fw:0, sam:1) 534s References: 534s >0 534s CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 534s /usr/bin/bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 534s @HD VN:1.5 SO:unsorted GO:query 534s @SQ SN:0 LN:55 534s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 534s r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:3 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^NN0N39 YT:Z:UU 534s Local alignment 1 (fw:1, sam:1) 534s References: 534s >0 534s TTGT 534s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 534s /usr/bin/bowtie2 --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 534s @HD VN:1.5 SO:unsorted GO:query 534s @SQ SN:0 LN:4 534s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 534s r0 0 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU 534s Local alignment 1 (fw:0, sam:1) 534s References: 534s >0 534s TTGT 534s /usr/bin/bowtie2 --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 534s @HD VN:1.5 SO:unsorted GO:query 534s @SQ SN:0 LN:4 534s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 534s r0 16 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU 534s Local alignment 2 (fw:1, sam:1) 534s References: 534s >0 534s TTGA 534s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 534s /usr/bin/bowtie2 --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 535s @HD VN:1.5 SO:unsorted GO:query 535s @SQ SN:0 LN:4 535s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 535s r0 0 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 535s Local alignment 2 (fw:0, sam:1) 535s References: 535s >0 535s TTGA 535s /usr/bin/bowtie2 --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 535s @HD VN:1.5 SO:unsorted GO:query 535s @SQ SN:0 LN:4 535s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 535s r0 16 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 535s Local alignment 3 (fw:1, sam:1) 535s References: 535s >0 535s TTGTTCGTTTGTTCGT 535s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 535s /usr/bin/bowtie2 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 535s @HD VN:1.5 SO:unsorted GO:query 535s @SQ SN:0 LN:16 535s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 535s r0 0 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 535s r0 256 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 535s Local alignment 3 (fw:0, sam:1) 535s References: 535s >0 535s TTGTTCGTTTGTTCGT 535s /usr/bin/bowtie2 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 535s @HD VN:1.5 SO:unsorted GO:query 535s @SQ SN:0 LN:16 535s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 535s r0 16 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 535s r0 272 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 535s Local alignment 4 (fw:1, sam:1) 535s References: 535s >0 535s TTGTTCGTTTGTTCGT 535s /usr/bin/bowtie2 --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 535s @HD VN:1.5 SO:unsorted GO:query 535s @SQ SN:0 LN:16 535s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 535s r0 0 0 1 37 12M * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:24 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 535s r0 256 0 9 255 8M4S * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 535s Local alignment 4 (fw:0, sam:1) 535s References: 535s >0 535s TTGTTCGTTTGTTCGT 535s /usr/bin/bowtie2 --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 535s @HD VN:1.5 SO:unsorted GO:query 535s @SQ SN:0 LN:16 535s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 535s r0 16 0 1 37 12M * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:24 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 535s r0 272 0 9 255 8M4S * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 535s Alignment order -k (fw:1, sam:1) 535s References: 535s >0 535s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 535s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 535s /usr/bin/bowtie2 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 536s @HD VN:1.5 SO:unsorted GO:query 536s @SQ SN:0 LN:86 536s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 536s r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 536s r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 536s r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 536s r0 256 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 536s Alignment order -k (fw:0, sam:1) 536s References: 536s >0 536s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 536s /usr/bin/bowtie2 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 536s @HD VN:1.5 SO:unsorted GO:query 536s @SQ SN:0 LN:86 536s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 536s r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 536s r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 536s r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 536s r0 272 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 536s Alignment order -a (fw:1, sam:1) 536s References: 536s >0 536s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 536s /usr/bin/bowtie2 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 536s @HD VN:1.5 SO:unsorted GO:query 536s @SQ SN:0 LN:86 536s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 536s r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 536s r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 536s r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 536s r0 256 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 536s Alignment order -a (fw:0, sam:1) 536s References: 536s >0 536s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 536s /usr/bin/bowtie2 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 536s @HD VN:1.5 SO:unsorted GO:query 536s @SQ SN:0 LN:86 536s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 536s r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 536s r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 536s r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 536s r0 272 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 536s Mate reporting order, -a (fw:1, sam:1) 536s References: 536s >0 536s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 536s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 536s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 536s @HD VN:1.5 SO:unsorted GO:query 536s @SQ SN:0 LN:407 536s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 536s r0 99 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r0 147 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r0 355 0 3 255 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r0 403 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r0 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r0 403 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r0 355 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r0 403 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r0 355 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r0 403 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r0 355 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r0 403 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r1 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r1 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r1 339 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r1 419 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r1 339 0 169 255 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r1 419 0 104 255 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r1 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r1 419 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r1 339 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r1 419 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r1 339 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r1 419 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 536s r2 99 0 307 255 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 536s r2 147 0 379 255 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 536s Mate reporting order, -a (fw:0, sam:1) 536s References: 536s >0 536s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 536s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 537s @HD VN:1.5 SO:unsorted GO:query 537s @SQ SN:0 LN:407 537s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 537s r0 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 339 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 419 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 339 0 169 255 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 419 0 104 255 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 419 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 339 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 419 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 339 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 419 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 99 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 147 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 355 0 3 255 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 403 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 403 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 355 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 403 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 355 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 403 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 355 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 403 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r2 83 0 379 255 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 537s r2 163 0 307 255 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 537s Mate reporting order, -M 1 (fw:1, sam:1) 537s References: 537s >0 537s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 537s /usr/bin/bowtie2 --fr --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 537s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 537s @HD VN:1.5 SO:unsorted GO:query 537s @SQ SN:0 LN:407 537s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 537s r0 99 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 147 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 83 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 163 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r2 99 0 307 42 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 537s r2 147 0 379 42 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 537s Mate reporting order, -M 1 (fw:0, sam:1) 537s References: 537s >0 537s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 537s /usr/bin/bowtie2 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 537s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 537s @HD VN:1.5 SO:unsorted GO:query 537s @SQ SN:0 LN:407 537s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 537s r0 83 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 163 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 99 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r1 147 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r2 83 0 379 42 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 537s r2 163 0 307 42 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 537s Non-overlapping; no args (fw:1, sam:1) 537s References: 537s >0 537s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 537s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 537s /usr/bin/bowtie2 --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 537s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 537s @HD VN:1.5 SO:unsorted GO:query 537s @SQ SN:0 LN:47 537s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 537s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 537s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s Non-overlapping; no args (fw:0, sam:1) 537s References: 537s >0 537s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 537s /usr/bin/bowtie2 --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 537s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 537s @HD VN:1.5 SO:unsorted GO:query 537s @SQ SN:0 LN:47 537s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 537s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 537s Non-overlapping; --no-discordant (fw:1, sam:1) 537s References: 537s >0 537s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 537s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 537s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 537s @HD VN:1.5 SO:unsorted GO:query 537s @SQ SN:0 LN:47 537s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 537s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 537s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s Non-overlapping; --no-discordant (fw:0, sam:1) 537s References: 537s >0 537s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 537s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 537s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 537s @HD VN:1.5 SO:unsorted GO:query 537s @SQ SN:0 LN:47 537s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 537s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 537s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 537s Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) 537s References: 537s >0 537s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 537s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 538s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:47 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 538s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 538s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 538s Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) 538s References: 538s >0 538s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 538s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 538s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:47 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 538s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 538s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 538s Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) 538s References: 538s >0 538s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 538s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 538s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:47 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 538s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 538s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 538s Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) 538s References: 538s >0 538s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 538s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 538s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:47 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 538s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 538s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 538s Non-overlapping; --no-dovetail (fw:1, sam:1) 538s References: 538s >0 538s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 538s /usr/bin/bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 538s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:47 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 538s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 538s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 538s Non-overlapping; --no-dovetail (fw:0, sam:1) 538s References: 538s >0 538s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 538s /usr/bin/bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 538s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:47 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 538s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 538s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 538s Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1) 538s References: 538s >0 538s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 538s /usr/bin/bowtie2 --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 538s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:47 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 538s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 538s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 538s Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1) 538s References: 538s >0 538s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 538s /usr/bin/bowtie2 --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 538s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:47 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 538s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 538s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 538s Non-overlapping; --no-overlap (fw:1, sam:1) 538s References: 538s >0 538s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 538s /usr/bin/bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 538s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:47 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 538s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 538s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 538s Non-overlapping; --no-overlap (fw:0, sam:1) 538s References: 538s >0 538s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 538s /usr/bin/bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 538s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:47 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 538s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 538s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 538s Overlapping; no args (fw:1, sam:1) 538s References: 538s >0 538s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 538s /usr/bin/bowtie2 --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 538s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 538s @HD VN:1.5 SO:unsorted GO:query 538s @SQ SN:0 LN:47 538s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 538s r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 538s r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 538s Overlapping; no args (fw:0, sam:1) 538s References: 538s >0 538s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 538s /usr/bin/bowtie2 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 539s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 539s @HD VN:1.5 SO:unsorted GO:query 539s @SQ SN:0 LN:47 539s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 539s r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 539s r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 539s Overlapping; --no-dovetail (fw:1, sam:1) 539s References: 539s >0 539s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 539s /usr/bin/bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 539s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 539s @HD VN:1.5 SO:unsorted GO:query 539s @SQ SN:0 LN:47 539s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 539s r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 539s r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 539s Overlapping; --no-dovetail (fw:0, sam:1) 539s References: 539s >0 539s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 539s /usr/bin/bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 539s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 539s @HD VN:1.5 SO:unsorted GO:query 539s @SQ SN:0 LN:47 539s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 539s r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 539s r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 539s Overlapping; --no-contain (fw:1, sam:1) 539s References: 539s >0 539s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 539s /usr/bin/bowtie2 --no-contain --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 539s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 539s @HD VN:1.5 SO:unsorted GO:query 539s @SQ SN:0 LN:47 539s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 539s r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 539s r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 539s Overlapping; --no-contain (fw:0, sam:1) 539s References: 539s >0 539s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 539s /usr/bin/bowtie2 --no-contain --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 539s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 539s @HD VN:1.5 SO:unsorted GO:query 539s @SQ SN:0 LN:47 539s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 539s r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 539s r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 539s Overlapping; --no-overlap (fw:1, sam:1) 539s References: 539s >0 539s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 539s /usr/bin/bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 539s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 539s @HD VN:1.5 SO:unsorted GO:query 539s @SQ SN:0 LN:47 539s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 539s r0 65 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP 539s r0 129 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:DP 539s Overlapping; --no-overlap (fw:0, sam:1) 539s References: 539s >0 539s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 539s /usr/bin/bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 540s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 540s @HD VN:1.5 SO:unsorted GO:query 540s @SQ SN:0 LN:47 540s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 540s r0 113 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:DP 540s r0 177 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP 540s Scoring params 1 (fw:1, sam:1) 540s References: 540s >0 540s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG 540s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 540s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 540s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 540s @HD VN:1.5 SO:unsorted GO:query 540s @SQ SN:0 LN:105 540s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 540s r0 0 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU 540s Scoring params 1 (fw:0, sam:1) 540s References: 540s >0 540s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG 540s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 540s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 540s @HD VN:1.5 SO:unsorted GO:query 540s @SQ SN:0 LN:105 540s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 540s r0 16 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU 540s Scoring params 2 (fw:1, sam:1) 540s References: 540s >0 540s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 540s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 540s /usr/bin/bowtie2 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 540s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 540s @HD VN:1.5 SO:unsorted GO:query 540s @SQ SN:0 LN:102 540s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 540s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 540s Scoring params 2 (fw:0, sam:1) 540s References: 540s >0 540s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 540s /usr/bin/bowtie2 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 540s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 540s @HD VN:1.5 SO:unsorted GO:query 540s @SQ SN:0 LN:102 540s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 540s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 540s Scoring params 3 (fw:1, sam:1) 540s References: 540s >0 540s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 540s /usr/bin/bowtie2 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 541s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 541s @HD VN:1.5 SO:unsorted GO:query 541s @SQ SN:0 LN:102 541s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 541s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 541s Scoring params 3 (fw:0, sam:1) 541s References: 541s >0 541s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 541s /usr/bin/bowtie2 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 541s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 541s @HD VN:1.5 SO:unsorted GO:query 541s @SQ SN:0 LN:102 541s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 541s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 541s Scoring params 4 (fw:1, sam:1) 541s References: 541s >0 541s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 541s /usr/bin/bowtie2 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 541s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 541s @HD VN:1.5 SO:unsorted GO:query 541s @SQ SN:0 LN:102 541s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 541s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 541s Scoring params 4 (fw:0, sam:1) 541s References: 541s >0 541s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 541s /usr/bin/bowtie2 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 541s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 541s @HD VN:1.5 SO:unsorted GO:query 541s @SQ SN:0 LN:102 541s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 541s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 541s Scoring params 5 (fw:1, sam:1) 541s References: 541s >0 541s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 541s /usr/bin/bowtie2 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 541s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 541s @HD VN:1.5 SO:unsorted GO:query 541s @SQ SN:0 LN:102 541s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 541s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-40 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 541s Scoring params 5 (fw:0, sam:1) 541s References: 541s >0 541s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 541s /usr/bin/bowtie2 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 541s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 541s @HD VN:1.5 SO:unsorted GO:query 541s @SQ SN:0 LN:102 541s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 541s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-40 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 541s Scoring params 6 (fw:1, sam:1) 541s References: 541s >0 541s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 541s /usr/bin/bowtie2 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 541s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 541s @HD VN:1.5 SO:unsorted GO:query 541s @SQ SN:0 LN:102 541s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 541s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 541s Scoring params 6 (fw:0, sam:1) 541s References: 541s >0 541s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 541s /usr/bin/bowtie2 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 541s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 541s @HD VN:1.5 SO:unsorted GO:query 541s @SQ SN:0 LN:102 541s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 541s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 541s Q XS:i 1a (fw:1, sam:1) 541s References: 541s >0 541s TTGTTCGATTGTTCGA 541s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 542s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 542s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 542s @HD VN:1.5 SO:unsorted GO:query 542s @SQ SN:0 LN:16 542s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 542s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 542s Q XS:i 1a (fw:0, sam:1) 542s References: 542s >0 542s TTGTTCGATTGTTCGA 542s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 542s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 542s @HD VN:1.5 SO:unsorted GO:query 542s @SQ SN:0 LN:16 542s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 542s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 542s Q XS:i 1a ! --mp 3,3 (fw:1, sam:1) 542s References: 542s >0 542s TTGTTCGATTGTTCGA 542s /usr/bin/bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 542s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 542s @HD VN:1.5 SO:unsorted GO:query 542s @SQ SN:0 LN:16 542s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 542s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 542s Q XS:i 1a ! --mp 3,3 (fw:0, sam:1) 542s References: 542s >0 542s TTGTTCGATTGTTCGA 542s /usr/bin/bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 542s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 542s @HD VN:1.5 SO:unsorted GO:query 542s @SQ SN:0 LN:16 542s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 542s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 542s Q XS:i 1a ! --mp 3,6 (fw:1, sam:1) 542s References: 542s >0 542s TTGTTCGATTGTTCGA 542s /usr/bin/bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 542s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 542s @HD VN:1.5 SO:unsorted GO:query 542s @SQ SN:0 LN:16 542s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 542s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 542s Q XS:i 1a ! --mp 3,6 (fw:0, sam:1) 542s References: 542s >0 542s TTGTTCGATTGTTCGA 542s /usr/bin/bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 542s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 542s @HD VN:1.5 SO:unsorted GO:query 542s @SQ SN:0 LN:16 542s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 542s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 542s Q XS:i 1a I --mp 3,3 (fw:1, sam:1) 542s References: 542s >0 542s TTGTTCGATTGTTCGA 542s /usr/bin/bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 542s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:16 543s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 543s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 543s Q XS:i 1a I --mp 3,3 (fw:0, sam:1) 543s References: 543s >0 543s TTGTTCGATTGTTCGA 543s /usr/bin/bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 543s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:16 543s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 543s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 543s Q XS:i 1a I --mp 3,6 (fw:1, sam:1) 543s References: 543s >0 543s TTGTTCGATTGTTCGA 543s /usr/bin/bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 543s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:16 543s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 543s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 543s Q XS:i 1a I --mp 3,6 (fw:0, sam:1) 543s References: 543s >0 543s TTGTTCGATTGTTCGA 543s /usr/bin/bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 543s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:16 543s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 543s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 543s Q XS:i 1a --ignore-quals (fw:1, sam:1) 543s References: 543s >0 543s TTGTTCGATTGTTCGA 543s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 543s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:16 543s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 543s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 543s Q XS:i 1a --ignore-quals (fw:0, sam:1) 543s References: 543s >0 543s TTGTTCGATTGTTCGA 543s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 543s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:16 543s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 543s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 543s Q XS:i 1b (fw:1, sam:1) 543s References: 543s >0 543s TTGTTCGATTGTTCGA 543s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 543s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:16 543s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 543s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-4 XS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 543s Q XS:i 1b (fw:0, sam:1) 543s References: 543s >0 543s TTGTTCGATTGTTCGA 543s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 543s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:16 543s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 543s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-4 XS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 543s Q XS:i 1b --ignore-quals (fw:1, sam:1) 543s References: 543s >0 543s TTGTTCGATTGTTCGA 543s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 543s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:16 543s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 543s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 543s Q XS:i 1b --ignore-quals (fw:0, sam:1) 543s References: 543s >0 543s TTGTTCGATTGTTCGA 543s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 543s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:16 543s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 543s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 543s Q XS:i 1c (fw:1, sam:1) 543s References: 543s >0 543s TTGTTCGATTGTTCGA 543s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 543s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:16 543s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 543s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 543s Q XS:i 1c (fw:0, sam:1) 543s References: 543s >0 543s TTGTTCGATTGTTCGA 543s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 543s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 543s @HD VN:1.5 SO:unsorted GO:query 543s @SQ SN:0 LN:16 543s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 543s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 543s Q XS:i 1c --ignore-quals (fw:1, sam:1) 543s References: 544s >0 544s TTGTTCGATTGTTCGA 544s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 544s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 544s @HD VN:1.5 SO:unsorted GO:query 544s @SQ SN:0 LN:16 544s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 544s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 544s Q XS:i 1c --ignore-quals (fw:0, sam:1) 544s References: 544s >0 544s TTGTTCGATTGTTCGA 544s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 544s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 544s @HD VN:1.5 SO:unsorted GO:query 544s @SQ SN:0 LN:16 544s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 544s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 544s (fw:1, sam:1) 544s References: 544s >0 544s CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT 544s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 544s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 544s @HD VN:1.5 SO:unsorted GO:query 544s @SQ SN:0 LN:68 544s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 544s r0 73 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP 544s r0 133 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 544s (fw:0, sam:1) 544s References: 544s >0 544s CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT 544s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 544s @HD VN:1.5 SO:unsorted GO:query 544s @SQ SN:0 LN:68 544s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 544s r0 137 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP 544s r0 69 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 544s (fw:1, sam:1) 544s References: 544s >0 544s TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT 544s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 544s /usr/bin/bowtie2 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 544s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 544s @HD VN:1.5 SO:unsorted GO:query 544s @SQ SN:0 LN:528 544s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 544s r0 0 0 217 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 544s (fw:0, sam:1) 544s References: 544s >0 544s TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT 544s /usr/bin/bowtie2 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 545s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 545s @HD VN:1.5 SO:unsorted GO:query 545s @SQ SN:0 LN:528 545s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 545s r0 16 0 89 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 545s (fw:1, sam:1) 545s References: 545s >0 545s TTGTTCGTTTGTTCGT 545s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 545s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 545s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 545s @HD VN:1.5 SO:unsorted GO:query 545s @SQ SN:0 LN:16 545s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 545s r0 0 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 545s (fw:0, sam:1) 545s References: 545s >0 545s TTGTTCGTTTGTTCGT 545s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 545s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 545s @HD VN:1.5 SO:unsorted GO:query 545s @SQ SN:0 LN:16 545s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 545s r0 16 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 545s (fw:1, sam:1) 545s References: 545s >0 545s TTGTTCGTTTGTTCGT 545s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 545s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 545s @HD VN:1.5 SO:unsorted GO:query 545s @SQ SN:0 LN:16 545s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 545s r0 0 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 545s (fw:0, sam:1) 545s References: 545s >0 545s TTGTTCGTTTGTTCGT 545s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 545s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 545s @HD VN:1.5 SO:unsorted GO:query 545s @SQ SN:0 LN:16 545s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 545s r0 16 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 545s XS:i 1 (fw:1, sam:1) 545s References: 545s >0 545s TTGTTCGATTGTTCGA 545s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 546s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 546s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 546s @HD VN:1.5 SO:unsorted GO:query 546s @SQ SN:0 LN:16 546s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 546s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 546s XS:i 1 (fw:0, sam:1) 546s References: 546s >0 546s TTGTTCGATTGTTCGA 546s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 546s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 546s @HD VN:1.5 SO:unsorted GO:query 546s @SQ SN:0 LN:16 546s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 546s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 546s XS:i 2 (fw:1, sam:1) 546s References: 546s >0 546s TTGTTCGATTGTTCGA 546s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 546s @HD VN:1.5 SO:unsorted GO:query 546s @SQ SN:0 LN:16 546s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 546s r0 4 * 0 0 * * 0 0 TTGTTCGT IIIIIIII YT:Z:UU 546s XS:i 2 (fw:0, sam:1) 546s References: 546s >0 546s TTGTTCGATTGTTCGA 546s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 546s @HD VN:1.5 SO:unsorted GO:query 546s @SQ SN:0 LN:16 546s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 546s r0 4 * 0 0 * * 0 0 ACGAACAA IIIIIIII YT:Z:UU 546s XS:i 3a (fw:1, sam:1) 546s References: 546s >0 546s TTGTTCGATTGTTCGT 546s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 546s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 546s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 546s @HD VN:1.5 SO:unsorted GO:query 546s @SQ SN:0 LN:16 546s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 546s r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 546s XS:i 3a (fw:0, sam:1) 546s References: 546s >0 546s TTGTTCGATTGTTCGT 546s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 547s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 547s @HD VN:1.5 SO:unsorted GO:query 547s @SQ SN:0 LN:16 547s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 547s r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 547s XS:i 3b (fw:1, sam:1) 547s References: 547s >0 547s TTGTTCGATTGTTCGT 547s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 547s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 547s @HD VN:1.5 SO:unsorted GO:query 547s @SQ SN:0 LN:16 547s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 547s r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 547s XS:i 3b (fw:0, sam:1) 547s References: 547s >0 547s TTGTTCGATTGTTCGT 547s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 547s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 547s @HD VN:1.5 SO:unsorted GO:query 547s @SQ SN:0 LN:16 547s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 547s r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 547s XS:i 3c (fw:1, sam:1) 547s References: 547s >0 547s TTGTTCGATTGTTCGT 547s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 547s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 547s @HD VN:1.5 SO:unsorted GO:query 547s @SQ SN:0 LN:16 547s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 547s r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 547s XS:i 3c (fw:0, sam:1) 547s References: 547s >0 547s TTGTTCGATTGTTCGT 547s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 547s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 547s @HD VN:1.5 SO:unsorted GO:query 547s @SQ SN:0 LN:16 547s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 547s r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 547s XS:i 4a (fw:1, sam:1) 547s References: 547s >0 547s TTGTTCAATTGTTCGATTGTTCGT 547s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 547s /usr/bin/bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 547s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 547s @HD VN:1.5 SO:unsorted GO:query 547s @SQ SN:0 LN:24 547s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 547s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 547s XS:i 4a (fw:0, sam:1) 547s References: 547s >0 547s TTGTTCAATTGTTCGATTGTTCGT 547s /usr/bin/bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 547s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 547s @HD VN:1.5 SO:unsorted GO:query 547s @SQ SN:0 LN:24 547s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 547s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 547s XS:i 4b (fw:1, sam:1) 547s References: 547s >0 547s TTGTTCAATTGTTCGATTGTTCGT 547s /usr/bin/bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 547s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 547s @HD VN:1.5 SO:unsorted GO:query 547s @SQ SN:0 LN:24 547s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 547s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 547s XS:i 4b (fw:0, sam:1) 547s References: 547s >0 547s TTGTTCAATTGTTCGATTGTTCGT 547s /usr/bin/bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 547s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 547s @HD VN:1.5 SO:unsorted GO:query 547s @SQ SN:0 LN:24 547s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 547s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 547s XS:i 5a (fw:1, sam:1) 547s References: 547s >0 547s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 547s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 548s /usr/bin/bowtie2 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 548s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 548s @HD VN:1.5 SO:unsorted GO:query 548s @SQ SN:0 LN:120 548s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 548s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 548s XS:i 5a (fw:0, sam:1) 548s References: 548s >0 548s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 548s /usr/bin/bowtie2 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 548s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 548s @HD VN:1.5 SO:unsorted GO:query 548s @SQ SN:0 LN:120 548s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 548s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 548s XS:i 5b (fw:1, sam:1) 548s References: 548s >0 548s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 548s /usr/bin/bowtie2 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 548s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 548s @HD VN:1.5 SO:unsorted GO:query 548s @SQ SN:0 LN:120 548s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 548s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 548s XS:i 5b (fw:0, sam:1) 548s References: 548s >0 548s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 548s /usr/bin/bowtie2 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 548s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 548s @HD VN:1.5 SO:unsorted GO:query 548s @SQ SN:0 LN:120 548s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 548s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 548s BWA-SW-like 1 (fw:1, sam:1) 548s References: 548s >0 548s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 548s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 548s /usr/bin/bowtie2 --bwa-sw-like --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 548s @HD VN:1.5 SO:unsorted GO:query 548s @SQ SN:0 LN:64 548s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 548s r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU 548s BWA-SW-like 1 (fw:0, sam:1) 548s References: 548s >0 548s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 548s /usr/bin/bowtie2 --bwa-sw-like --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 549s @HD VN:1.5 SO:unsorted GO:query 549s @SQ SN:0 LN:64 549s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 549s r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU 549s BWA-SW-like 2 (fw:1, sam:1) 549s References: 549s >0 549s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 549s /usr/bin/bowtie2 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 549s @HD VN:1.5 SO:unsorted GO:query 549s @SQ SN:0 LN:64 549s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 549s r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU 549s BWA-SW-like 2 (fw:0, sam:1) 549s References: 549s >0 549s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 549s /usr/bin/bowtie2 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 549s @HD VN:1.5 SO:unsorted GO:query 549s @SQ SN:0 LN:64 549s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 549s r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU 549s BWA-SW-like 3 (fw:1, sam:1) 549s References: 549s >0 549s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 549s /usr/bin/bowtie2 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 549s @HD VN:1.5 SO:unsorted GO:query 549s @SQ SN:0 LN:64 549s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 549s r0 0 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU 549s BWA-SW-like 3 (fw:0, sam:1) 549s References: 549s >0 549s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 549s /usr/bin/bowtie2 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 549s @HD VN:1.5 SO:unsorted GO:query 549s @SQ SN:0 LN:64 549s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 549s r0 16 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU 549s SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1) 549s References: 549s >0 549s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 549s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 549s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 550s @HD VN:1.5 SO:unsorted GO:query 550s @SQ SN:0 LN:69 550s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 550s r0 99 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 550s r0 147 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 550s SAM paired-end where both alignments start at the same offset (ff case) (fw:1, sam:1) 550s References: 550s >0 550s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 550s /usr/bin/bowtie2 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 550s @HD VN:1.5 SO:unsorted GO:query 550s @SQ SN:0 LN:69 550s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 550s r0 67 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 550s r0 131 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 550s SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1) 550s References: 550s >0 550s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 550s /usr/bin/bowtie2 --rf --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 550s @HD VN:1.5 SO:unsorted GO:query 550s @SQ SN:0 LN:69 550s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 550s r0 83 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 550s r0 163 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 550s SAM paired-end where both mates align 1 (fw:1, sam:1) 550s References: 550s >0 550s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 550s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 550s @HD VN:1.5 SO:unsorted GO:query 550s @SQ SN:0 LN:69 550s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 550s r0 99 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP 550s r0 147 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP 550s SAM paired-end where both mates align 2 (fw:1, sam:1) 550s References: 550s >0 550s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 550s /usr/bin/bowtie2 --rf --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 550s @HD VN:1.5 SO:unsorted GO:query 550s @SQ SN:0 LN:69 550s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 550s r0 83 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP 550s r0 163 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP 550s SAM paired-end where both mates align 3 (fw:1, sam:1) 550s References: 550s >0 550s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 550s /usr/bin/bowtie2 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 550s @HD VN:1.5 SO:unsorted GO:query 550s @SQ SN:0 LN:69 550s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 550s r0 67 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP 550s r0 131 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP 550s SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1) 550s References: 550s >0 550s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 550s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 550s @HD VN:1.5 SO:unsorted GO:query 550s @SQ SN:0 LN:69 550s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 550s r0 73 0 4 255 24M = 4 0 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YT:Z:UP 550s r0 133 0 4 0 * = 4 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 550s SAM paired-end where neither mate aligns (fw:1, sam:1) 550s References: 550s >0 550s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 550s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 550s @HD VN:1.5 SO:unsorted GO:query 550s @SQ SN:0 LN:69 550s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 550s r0 77 * 0 0 * * 0 0 CTATATACGAAAAAGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 550s r0 141 * 0 0 * * 0 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 550s SAM paired-end where both mates align, but discordantly (fw:1, sam:1) 550s References: 550s >0 550s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 550s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 550s @HD VN:1.5 SO:unsorted GO:query 550s @SQ SN:0 LN:69 550s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 550s r0 65 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YS:i:0 YT:Z:DP 550s r0 129 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP 550s matchesRef regression 4 (fw:1, sam:1) 550s References: 550s >0 550s CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC 550s >1 550s GCTCGGAATTCGTGCTCCGNCCCGTACGGTT 550s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 551s /usr/bin/bowtie2 --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 551s @HD VN:1.5 SO:unsorted GO:query 551s @SQ SN:0 LN:120 551s @SQ SN:1 LN:31 551s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 551s r0 4 * 0 0 * * 0 0 ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU 551s matchesRef regression 4 (fw:0, sam:1) 551s References: 551s >0 551s CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC 551s >1 551s GCTCGGAATTCGTGCTCCGNCCCGTACGGTT 551s /usr/bin/bowtie2 --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 551s @HD VN:1.5 SO:unsorted GO:query 551s @SQ SN:0 LN:120 551s @SQ SN:1 LN:31 551s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 551s r0 4 * 0 0 * * 0 0 GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU 551s matchesRef regression 3 (fw:1, sam:1) 551s References: 551s >0 551s GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC 551s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 551s /usr/bin/bowtie2 --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 551s @HD VN:1.5 SO:unsorted GO:query 551s @SQ SN:0 LN:53 551s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 551s r0 16 0 10 255 38M * 0 0 CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UU 551s matchesRef regression 3 (fw:0, sam:1) 551s References: 551s >0 551s GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC 551s /usr/bin/bowtie2 --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 551s @HD VN:1.5 SO:unsorted GO:query 551s @SQ SN:0 LN:53 551s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 551s r0 0 0 10 255 38M * 0 0 CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UU 551s matchesRef regression 2 (fw:1, sam:1) 551s References: 551s >0 551s GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG 551s >1 551s CCTTGTTNTTAATGCTGCCTGGTTTNG 551s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 552s /usr/bin/bowtie2 --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 552s @HD VN:1.5 SO:unsorted GO:query 552s @SQ SN:0 LN:47 552s @SQ SN:1 LN:27 552s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 552s r0 77 * 0 0 * * 0 0 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 552s r0 141 * 0 0 * * 0 0 ACATATCCAGAGCTGCCGACAACGAAATGAACCCGAGAGCACAAATCCAGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 552s matchesRef regression 2 (fw:0, sam:1) 552s References: 552s >0 552s GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG 552s >1 552s CCTTGTTNTTAATGCTGCCTGGTTTNG 552s /usr/bin/bowtie2 --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 552s @HD VN:1.5 SO:unsorted GO:query 552s @SQ SN:0 LN:47 552s @SQ SN:1 LN:27 552s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 552s r0 83 0 1 255 29S23M = 1 -68 CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-78 XN:i:7 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:-128 YT:Z:CP 552s r0 163 0 1 255 45S15M = 1 68 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-128 XN:i:9 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:14T0 YS:i:-78 YT:Z:CP 552s matchesRef regression 1 (fw:1, sam:1) 552s References: 552s >0 552s AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC 552s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 552s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 552s @HD VN:1.5 SO:unsorted GO:query 552s @SQ SN:0 LN:61 552s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 552s r0 0 0 12 255 50M10S * 0 0 AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:9 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU 552s matchesRef regression 1 (fw:0, sam:1) 552s References: 552s >0 552s AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC 552s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 552s @HD VN:1.5 SO:unsorted GO:query 552s @SQ SN:0 LN:61 552s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 552s r0 16 0 12 255 50M10S * 0 0 AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:9 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU 552s Discordant with different chromosomes (fw:1, sam:1) 552s References: 552s >0 552s TTTATAAAAATATTTCCCCCCCC 552s >1 552s CCCCCCTGTCGCTACCGCCCCCCCCCCC 552s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 553s /usr/bin/bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 553s @HD VN:1.5 SO:unsorted GO:query 553s @SQ SN:0 LN:23 553s @SQ SN:1 LN:28 553s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 553s r0 65 0 4 255 10M 1 8 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 553s r0 129 1 8 255 10M 0 4 0 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 553s r1 65 0 4 255 10M 1 7 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 553s r1 129 1 7 255 10M 0 4 0 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 553s Discordant with different chromosomes (fw:0, sam:1) 553s References: 553s >0 553s TTTATAAAAATATTTCCCCCCCC 553s >1 553s CCCCCCTGTCGCTACCGCCCCCCCCCCC 553s /usr/bin/bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 553s @HD VN:1.5 SO:unsorted GO:query 553s @SQ SN:0 LN:23 553s @SQ SN:1 LN:28 553s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 553s r0 113 1 8 255 10M 0 4 0 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 553s r0 177 0 4 255 10M 1 8 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 553s r1 113 1 7 255 10M 0 4 0 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 553s r1 177 0 4 255 10M 1 7 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 553s (fw:1, sam:1) 553s References: 553s >0 553s AGCATCGATCAGTATCTGA 553s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 553s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 553s @HD VN:1.5 SO:unsorted GO:query 553s @SQ SN:0 LN:19 553s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 553s r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 553s (fw:0, sam:1) 553s References: 553s >0 553s AGCATCGATCAGTATCTGA 553s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 553s @HD VN:1.5 SO:unsorted GO:query 553s @SQ SN:0 LN:19 553s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 553s r1 16 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 553s (fw:1, sam:1) 553s References: 553s >0 553s AGCATCGATCAGTATCTGA 553s /usr/bin/bowtie2 -s 1 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 553s @HD VN:1.5 SO:unsorted GO:query 553s @SQ SN:0 LN:19 553s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 553s r1 99 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 553s r1 147 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 553s (fw:0, sam:1) 553s References: 553s >0 553s AGCATCGATCAGTATCTGA 553s /usr/bin/bowtie2 -s 1 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 553s @HD VN:1.5 SO:unsorted GO:query 553s @SQ SN:0 LN:19 553s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 553s r1 83 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 553s r1 163 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 553s (fw:1, sam:1) 553s References: 553s >0 553s AGCATCGATCAGTATCTGA 553s /usr/bin/bowtie2 -s 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 554s @HD VN:1.5 SO:unsorted GO:query 554s @SQ SN:0 LN:19 554s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 554s (fw:0, sam:1) 554s References: 554s >0 554s AGCATCGATCAGTATCTGA 554s /usr/bin/bowtie2 -s 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 554s @HD VN:1.5 SO:unsorted GO:query 554s @SQ SN:0 LN:19 554s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 554s (fw:1, sam:1) 554s References: 554s >0 554s AGCATCGATCAGTATCTGA 554s /usr/bin/bowtie2 -s 2 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 554s @HD VN:1.5 SO:unsorted GO:query 554s @SQ SN:0 LN:19 554s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 554s (fw:0, sam:1) 554s References: 554s >0 554s AGCATCGATCAGTATCTGA 554s /usr/bin/bowtie2 -s 2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 554s @HD VN:1.5 SO:unsorted GO:query 554s @SQ SN:0 LN:19 554s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 554s (fw:1, sam:1) 554s References: 554s >0 554s AGCATCGATCAGTATCTGA 554s /usr/bin/bowtie2 -s 1 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 554s @HD VN:1.5 SO:unsorted GO:query 554s @SQ SN:0 LN:19 554s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 554s r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 554s (fw:0, sam:1) 554s References: 554s >0 554s AGCATCGATCAGTATCTGA 554s /usr/bin/bowtie2 -s 1 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 554s @HD VN:1.5 SO:unsorted GO:query 554s @SQ SN:0 LN:19 554s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 554s r1 16 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 554s (fw:1, sam:1) 554s References: 554s >0 554s AGCATCGATCAGTATCTGA 554s /usr/bin/bowtie2 -s 1 --trim3 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 554s @HD VN:1.5 SO:unsorted GO:query 554s @SQ SN:0 LN:19 554s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 554s r1 0 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 554s (fw:0, sam:1) 554s References: 554s >0 554s AGCATCGATCAGTATCTGA 554s /usr/bin/bowtie2 -s 1 --trim3 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 554s @HD VN:1.5 SO:unsorted GO:query 554s @SQ SN:0 LN:19 554s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 554s r1 16 0 6 255 9M * 0 0 CGATCAGTA IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 554s (fw:0, sam:1) 554s References: 554s >0 554s AGCATCGATCAGTATCTGA 554s /usr/bin/bowtie2 -s 1 --trim5 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 554s @HD VN:1.5 SO:unsorted GO:query 554s @SQ SN:0 LN:19 554s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 554s r1 16 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 554s (fw:1, sam:1) 554s References: 554s >0 554s AGCATCGATCAGTATCTGA 554s /usr/bin/bowtie2 -s 1 --trim5 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 555s @HD VN:1.5 SO:unsorted GO:query 555s @SQ SN:0 LN:19 555s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 555s r1 0 0 6 255 9M * 0 0 CGATCAGTA IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 555s (fw:1, sam:1) 555s References: 555s >0 555s TGC 555s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 555s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 555s @HD VN:1.5 SO:unsorted GO:query 555s @SQ SN:0 LN:3 555s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 555s r0 0 0 1 255 1S3M * 0 0 ATGC IIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 555s (fw:0, sam:1) 555s References: 555s >0 555s TGC 555s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 555s @HD VN:1.5 SO:unsorted GO:query 555s @SQ SN:0 LN:3 555s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 555s r0 16 0 1 255 1S3M * 0 0 ATGC IIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 555s (fw:1, sam:1) 555s References: 555s >0 555s TTGTTCGT 555s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 556s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 556s @HD VN:1.5 SO:unsorted GO:query 556s @SQ SN:0 LN:8 556s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 556s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 556s (fw:0, sam:1) 556s References: 556s >0 556s TTGTTCGT 556s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 556s @HD VN:1.5 SO:unsorted GO:query 556s @SQ SN:0 LN:8 556s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 556s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 556s (fw:1, sam:1) 556s References: 556s >0 556s TTGTTCGT 556s /usr/bin/bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 556s @HD VN:1.5 SO:unsorted GO:query 556s @SQ SN:0 LN:8 556s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 556s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 556s (fw:0, sam:1) 556s References: 556s >0 556s TTGTTCGT 556s /usr/bin/bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 556s @HD VN:1.5 SO:unsorted GO:query 556s @SQ SN:0 LN:8 556s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 556s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 556s (fw:1, sam:1) 556s References: 556s >0 556s TTGTTCGT 556s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 556s @HD VN:1.5 SO:unsorted GO:query 556s @SQ SN:0 LN:8 556s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 556s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 556s r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 556s (fw:0, sam:1) 556s References: 556s >0 556s TTGTTCGT 556s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 556s @HD VN:1.5 SO:unsorted GO:query 556s @SQ SN:0 LN:8 556s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 556s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 556s r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 556s (fw:1, sam:1) 556s References: 556s >0 556s TTGTTCGT 556s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 556s @HD VN:1.5 SO:unsorted GO:query 556s @SQ SN:0 LN:8 556s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 556s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 556s r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 556s (fw:0, sam:1) 556s References: 556s >0 556s TTGTTCGT 556s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 557s @HD VN:1.5 SO:unsorted GO:query 557s @SQ SN:0 LN:8 557s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 557s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 557s r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 557s (fw:1, sam:1) 557s References: 557s >0 557s TTGTTCGT 557s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 557s @HD VN:1.5 SO:unsorted GO:query 557s @SQ SN:0 LN:8 557s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 557s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 557s r1 0 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 557s r2 0 0 1 255 1S6M * 0 0 ATTGTTC IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 557s (fw:0, sam:1) 557s References: 557s >0 557s TTGTTCGT 557s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 557s @HD VN:1.5 SO:unsorted GO:query 557s @SQ SN:0 LN:8 557s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 557s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 557s r1 16 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 557s r2 16 0 1 255 1S6M * 0 0 ATTGTTC IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 557s (fw:1, sam:1) 557s References: 557s >0 557s TTGTTCGT 557s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz 557s @HD VN:1.5 SO:unsorted GO:query 557s @SQ SN:0 LN:8 557s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" 557s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 557s r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 557s r2 4 * 0 0 * * 0 0 GTTCGTA IIIIIII YT:Z:UU 557s r3 4 * 0 0 * * 0 0 ATTGTTC IIIIIII YT:Z:UU 557s (fw:0, sam:1) 557s References: 557s >0 557s TTGTTCGT 557s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz 557s @HD VN:1.5 SO:unsorted GO:query 557s @SQ SN:0 LN:8 557s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" 557s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 557s r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 557s r2 4 * 0 0 * * 0 0 TACGAAC IIIIIII YT:Z:UU 557s r3 4 * 0 0 * * 0 0 GAACAAT IIIIIII YT:Z:UU 557s (fw:1, sam:1) 557s References: 557s >0 557s TTGTTCGT 557s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 557s @HD VN:1.5 SO:unsorted GO:query 557s @SQ SN:0 LN:8 557s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 557s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 557s (fw:0, sam:1) 557s References: 557s >0 557s TTGTTCGT 557s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 557s @HD VN:1.5 SO:unsorted GO:query 557s @SQ SN:0 LN:8 557s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 557s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 557s (fw:1, sam:1) 557s References: 557s >0 557s TTGTTCGT 557s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 558s @HD VN:1.5 SO:unsorted GO:query 558s @SQ SN:0 LN:8 558s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 558s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 558s (fw:0, sam:1) 558s References: 558s >0 558s TTGTTCGT 558s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 558s @HD VN:1.5 SO:unsorted GO:query 558s @SQ SN:0 LN:8 558s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 558s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 558s P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) 558s References: 558s >0 558s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 558s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 558s /usr/bin/bowtie2 -X 1000 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 558s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 558s @HD VN:1.5 SO:unsorted GO:query 558s @SQ SN:0 LN:1000 558s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 558s r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 558s r0 147 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 558s P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) 558s References: 558s >0 558s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 558s /usr/bin/bowtie2 -X 1000 --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 558s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 558s @HD VN:1.5 SO:unsorted GO:query 558s @SQ SN:0 LN:1000 558s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 558s r0 83 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 558s r0 163 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 558s P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) 558s References: 558s >0 558s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 558s /usr/bin/bowtie2 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 559s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 559s @HD VN:1.5 SO:unsorted GO:query 559s @SQ SN:0 LN:1000 559s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 559s r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 559s r0 147 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 559s P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1) 559s References: 559s >0 559s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 559s /usr/bin/bowtie2 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 559s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 559s @HD VN:1.5 SO:unsorted GO:query 559s @SQ SN:0 LN:1000 559s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 559s r0 83 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 559s r0 163 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 559s P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) 559s References: 559s >0 559s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 559s /usr/bin/bowtie2 -X 1000 --fr --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 559s @HD VN:1.5 SO:unsorted GO:query 559s @SQ SN:0 LN:1000 559s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 559s r0 99 0 13 1 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 559s r0 147 0 553 1 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 559s r0 355 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 559s r0 403 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 559s r0 355 0 13 255 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 559s r0 403 0 790 255 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 559s r0 355 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 559s r0 403 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 559s r0 355 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 559s r0 403 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 559s P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) 559s References: 559s >0 559s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 559s /usr/bin/bowtie2 -X 1000 --fr --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 559s @HD VN:1.5 SO:unsorted GO:query 559s @SQ SN:0 LN:1000 559s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 559s r0 83 0 553 1 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 559s r0 163 0 13 1 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 559s r0 339 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 559s r0 419 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 559s r0 339 0 790 255 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 559s r0 419 0 13 255 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 559s r0 339 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 559s r0 419 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 559s r0 339 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 559s r0 419 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 559s P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) 559s References: 559s >0 559s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 559s /usr/bin/bowtie2 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 559s @HD VN:1.5 SO:unsorted GO:query 559s @SQ SN:0 LN:1000 559s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 559s r0 99 0 13 1 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 559s r0 147 0 553 1 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 559s r0 355 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 559s r0 403 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 559s r0 355 0 13 255 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 559s r0 403 0 790 255 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 559s r0 355 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 559s r0 403 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 559s r0 355 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 559s r0 403 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 559s P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1) 559s References: 559s >0 559s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 559s /usr/bin/bowtie2 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 560s @HD VN:1.5 SO:unsorted GO:query 560s @SQ SN:0 LN:1000 560s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 560s r0 83 0 553 1 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 560s r0 163 0 13 1 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 560s r0 339 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 560s r0 419 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 560s r0 339 0 790 255 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 560s r0 419 0 13 255 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 560s r0 339 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 560s r0 419 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 560s r0 339 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 560s r0 419 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 560s P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 560s References: 560s >0 560s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 560s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 560s /usr/bin/bowtie2 -X 150 --fr --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 560s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 560s @HD VN:1.5 SO:unsorted GO:query 560s @SQ SN:0 LN:363 560s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 560s r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 560s r0 147 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 560s P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 560s References: 560s >0 560s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 560s /usr/bin/bowtie2 -X 150 --fr --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 560s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 560s @HD VN:1.5 SO:unsorted GO:query 560s @SQ SN:0 LN:363 560s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 560s r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 560s r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 560s P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 560s References: 560s >0 560s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 560s /usr/bin/bowtie2 --local -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 560s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 560s @HD VN:1.5 SO:unsorted GO:query 560s @SQ SN:0 LN:363 560s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 560s r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 560s r0 147 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 560s P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 560s References: 560s >0 560s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 560s /usr/bin/bowtie2 --local -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 560s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 560s @HD VN:1.5 SO:unsorted GO:query 560s @SQ SN:0 LN:363 560s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 560s r0 83 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 560s r0 163 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 560s P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 560s References: 560s >0 560s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 560s /usr/bin/bowtie2 -X 150 --fr --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 561s @HD VN:1.5 SO:unsorted GO:query 561s @SQ SN:0 LN:363 561s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 561s r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 561s P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 561s References: 561s >0 561s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 561s /usr/bin/bowtie2 -X 150 --fr --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 561s @HD VN:1.5 SO:unsorted GO:query 561s @SQ SN:0 LN:363 561s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 561s r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 561s P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 561s References: 561s >0 561s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 561s /usr/bin/bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 561s @HD VN:1.5 SO:unsorted GO:query 561s @SQ SN:0 LN:363 561s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 561s r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 561s P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 561s References: 561s >0 561s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 561s /usr/bin/bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 561s @HD VN:1.5 SO:unsorted GO:query 561s @SQ SN:0 LN:363 561s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 561s r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 561s P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 561s References: 561s >0 561s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 561s /usr/bin/bowtie2 --fr --quiet -M 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 561s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 561s @HD VN:1.5 SO:unsorted GO:query 561s @SQ SN:0 LN:363 561s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 561s r0 147 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 561s P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 561s References: 561s >0 561s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 561s /usr/bin/bowtie2 --fr --quiet -M 1 -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 561s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 561s @HD VN:1.5 SO:unsorted GO:query 561s @SQ SN:0 LN:363 561s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s r0 83 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 561s r0 163 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 561s P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 561s References: 561s >0 561s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 561s /usr/bin/bowtie2 --fr --quiet -M 1 --local -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 561s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 561s @HD VN:1.5 SO:unsorted GO:query 561s @SQ SN:0 LN:363 561s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 561s r0 147 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 561s P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 561s References: 561s >0 561s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 561s /usr/bin/bowtie2 --fr --quiet -M 1 --local -X 150 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 561s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 561s @HD VN:1.5 SO:unsorted GO:query 561s @SQ SN:0 LN:363 561s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s r0 83 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 561s r0 163 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 561s P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) 561s References: 561s >0 561s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 561s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 561s /usr/bin/bowtie2 --fr --quiet -k 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 561s @HD VN:1.5 SO:unsorted GO:query 561s @SQ SN:0 LN:126 561s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 561s r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 561s P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) 561s References: 561s >0 561s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 561s /usr/bin/bowtie2 --fr --quiet -k 1 -X 150 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 561s @HD VN:1.5 SO:unsorted GO:query 561s @SQ SN:0 LN:126 561s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 561s r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 561s r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 561s P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) 561s References: 561s >0 561s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 561s /usr/bin/bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 562s @HD VN:1.5 SO:unsorted GO:query 562s @SQ SN:0 LN:126 562s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 562s r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 562s r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 562s P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) 562s References: 562s >0 562s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 562s /usr/bin/bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 562s @HD VN:1.5 SO:unsorted GO:query 562s @SQ SN:0 LN:126 562s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 562s r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 562s r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 562s P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) 562s References: 562s >0 562s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 562s /usr/bin/bowtie2 -X 150 --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 562s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 562s @HD VN:1.5 SO:unsorted GO:query 562s @SQ SN:0 LN:126 562s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 562s r0 99 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 562s r0 147 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 562s P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) 562s References: 562s >0 562s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 562s /usr/bin/bowtie2 -X 150 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 562s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 562s @HD VN:1.5 SO:unsorted GO:query 562s @SQ SN:0 LN:126 562s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 562s r0 83 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 562s r0 163 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 562s P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) 562s References: 562s >0 562s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 562s /usr/bin/bowtie2 -X 150 --local --fr --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 562s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 562s @HD VN:1.5 SO:unsorted GO:query 562s @SQ SN:0 LN:126 562s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 562s r0 99 0 13 44 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 562s r0 147 0 79 44 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 562s P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) 562s References: 562s >0 562s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 562s /usr/bin/bowtie2 -X 150 --local --fr --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 562s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 562s @HD VN:1.5 SO:unsorted GO:query 562s @SQ SN:0 LN:126 562s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 562s r0 83 0 79 44 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 562s r0 163 0 13 44 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 562s P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 562s References: 562s >0 562s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA 562s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 563s /usr/bin/bowtie2 -X 150 --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 563s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 563s @HD VN:1.5 SO:unsorted GO:query 563s @SQ SN:0 LN:2607 563s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 563s r0 99 0 1435 1 33M = 1501 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 563s r0 147 0 1501 1 28M = 1435 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 563s P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 563s References: 563s >0 563s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA 563s /usr/bin/bowtie2 -X 150 --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 563s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 563s @HD VN:1.5 SO:unsorted GO:query 563s @SQ SN:0 LN:2607 563s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 563s r0 83 0 790 1 28M = 724 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 563s r0 163 0 724 1 33M = 790 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 563s P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:1, sam:1) 563s References: 563s >0 563s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC 563s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 563s /usr/bin/bowtie2 --local -X 150 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 564s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 564s @HD VN:1.5 SO:unsorted GO:query 564s @SQ SN:0 LN:1906 564s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 564s r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 564s r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 564s P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1) 564s References: 564s >0 564s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC 564s /usr/bin/bowtie2 --local -X 150 --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 564s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 564s @HD VN:1.5 SO:unsorted GO:query 564s @SQ SN:0 LN:1906 564s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 564s r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 564s r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 564s U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1) 564s References: 564s >0 564s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 564s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 564s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 564s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 564s @HD VN:1.5 SO:unsorted GO:query 564s @SQ SN:0 LN:56 564s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 564s r0 0 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 564s U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1) 564s References: 564s >0 564s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 564s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 564s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 564s @HD VN:1.5 SO:unsorted GO:query 564s @SQ SN:0 LN:56 564s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 564s r0 16 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 564s U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1) 564s References: 564s >0 564s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 564s /usr/bin/bowtie2 --local --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 565s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 565s @HD VN:1.5 SO:unsorted GO:query 565s @SQ SN:0 LN:56 565s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 565s r0 0 0 13 44 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 565s U.M.1.L. Unpaired -M w/ 1 hit local (fw:0, sam:1) 565s References: 565s >0 565s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 565s /usr/bin/bowtie2 --local --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 565s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 565s @HD VN:1.5 SO:unsorted GO:query 565s @SQ SN:0 LN:56 565s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 565s r0 16 0 13 44 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 565s U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:1, sam:1) 565s References: 565s >0 565s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 565s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 565s @HD VN:1.5 SO:unsorted GO:query 565s @SQ SN:0 LN:56 565s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 565s r0 0 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 565s U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:0, sam:1) 565s References: 565s >0 565s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 565s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 565s @HD VN:1.5 SO:unsorted GO:query 565s @SQ SN:0 LN:56 565s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 565s r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 565s U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1) 565s References: 565s >0 565s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 565s /usr/bin/bowtie2 --local --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 565s @HD VN:1.5 SO:unsorted GO:query 565s @SQ SN:0 LN:56 565s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 565s r0 0 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 565s U.M.1.L. Unpaired -m w/ 1 hit local (fw:0, sam:1) 565s References: 565s >0 565s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 565s /usr/bin/bowtie2 --local --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 565s @HD VN:1.5 SO:unsorted GO:query 565s @SQ SN:0 LN:56 565s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 565s r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 565s U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1) 565s References: 565s >0 565s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 565s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 565s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 565s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 565s @HD VN:1.5 SO:unsorted GO:query 565s @SQ SN:0 LN:85 565s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 565s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 565s U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1) 565s References: 565s >0 565s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 565s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 565s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 565s @HD VN:1.5 SO:unsorted GO:query 565s @SQ SN:0 LN:85 565s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 565s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 565s U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1) 565s References: 565s >0 565s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 565s /usr/bin/bowtie2 --local --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 566s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 566s @HD VN:1.5 SO:unsorted GO:query 566s @SQ SN:0 LN:85 566s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 566s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 566s U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1) 566s References: 566s >0 566s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 566s /usr/bin/bowtie2 --local --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 566s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 566s @HD VN:1.5 SO:unsorted GO:query 566s @SQ SN:0 LN:85 566s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 566s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 566s U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:1, sam:1) 566s References: 566s >0 566s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 566s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 566s @HD VN:1.5 SO:unsorted GO:query 566s @SQ SN:0 LN:85 566s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 566s r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 566s U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1) 566s References: 566s >0 566s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 566s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 566s @HD VN:1.5 SO:unsorted GO:query 566s @SQ SN:0 LN:85 566s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 566s r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 566s U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1) 566s References: 566s >0 566s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 566s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 566s @HD VN:1.5 SO:unsorted GO:query 566s @SQ SN:0 LN:85 566s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 566s r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 566s U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1) 566s References: 566s >0 566s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 566s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 566s @HD VN:1.5 SO:unsorted GO:query 566s @SQ SN:0 LN:85 566s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 566s r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 566s U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1) 566s References: 566s >0 566s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 566s /usr/bin/bowtie2 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 566s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 566s @HD VN:1.5 SO:unsorted GO:query 566s @SQ SN:0 LN:85 566s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 566s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 566s U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1) 566s References: 566s >0 566s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 566s /usr/bin/bowtie2 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 566s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 566s @HD VN:1.5 SO:unsorted GO:query 566s @SQ SN:0 LN:85 566s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 566s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 566s U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1) 566s References: 566s >0 566s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 566s /usr/bin/bowtie2 --quiet -M 2 --local --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 566s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 566s @HD VN:1.5 SO:unsorted GO:query 566s @SQ SN:0 LN:85 566s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 566s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 566s U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1) 566s References: 566s >0 566s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 566s /usr/bin/bowtie2 --quiet -M 2 --local --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 567s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 567s @HD VN:1.5 SO:unsorted GO:query 567s @SQ SN:0 LN:85 567s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 567s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 567s U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1) 567s References: 567s >0 567s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 567s /usr/bin/bowtie2 --quiet -k 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 567s @HD VN:1.5 SO:unsorted GO:query 567s @SQ SN:0 LN:85 567s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 567s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 567s r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 567s U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:0, sam:1) 567s References: 567s >0 567s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 567s /usr/bin/bowtie2 --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 567s @HD VN:1.5 SO:unsorted GO:query 567s @SQ SN:0 LN:85 567s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 567s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 567s r0 272 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 567s U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1) 567s References: 567s >0 567s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 567s /usr/bin/bowtie2 --local --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 567s @HD VN:1.5 SO:unsorted GO:query 567s @SQ SN:0 LN:85 567s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 567s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 567s r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 567s U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:0, sam:1) 567s References: 567s >0 567s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 567s /usr/bin/bowtie2 --local --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 567s @HD VN:1.5 SO:unsorted GO:query 567s @SQ SN:0 LN:85 567s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 567s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 567s r0 272 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 567s U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 567s References: 567s >0 567s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 567s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 567s /usr/bin/bowtie2 -X 150 --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 567s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 568s @HD VN:1.5 SO:unsorted GO:query 568s @SQ SN:0 LN:340 568s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 568s r0 0 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 568s References: 568s >0 568s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 568s /usr/bin/bowtie2 -X 150 --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 568s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 568s @HD VN:1.5 SO:unsorted GO:query 568s @SQ SN:0 LN:340 568s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 568s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 568s References: 568s >0 568s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 568s /usr/bin/bowtie2 --local --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 568s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 568s @HD VN:1.5 SO:unsorted GO:query 568s @SQ SN:0 LN:340 568s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 568s r0 0 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 568s References: 568s >0 568s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 568s /usr/bin/bowtie2 --local --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 568s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 568s @HD VN:1.5 SO:unsorted GO:query 568s @SQ SN:0 LN:340 568s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 568s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1) 568s References: 568s >0 568s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 568s /usr/bin/bowtie2 --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 568s @HD VN:1.5 SO:unsorted GO:query 568s @SQ SN:0 LN:340 568s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 568s r0 0 0 304 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 256 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 256 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 256 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 256 0 219 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:0, sam:1) 568s References: 568s >0 568s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 568s /usr/bin/bowtie2 --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 568s @HD VN:1.5 SO:unsorted GO:query 568s @SQ SN:0 LN:340 568s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 568s r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 272 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 272 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 272 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 272 0 219 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:1, sam:1) 568s References: 568s >0 568s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 568s /usr/bin/bowtie2 --local --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 568s @HD VN:1.5 SO:unsorted GO:query 568s @SQ SN:0 LN:340 568s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 568s r0 0 0 304 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 256 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 256 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 256 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 256 0 219 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:0, sam:1) 568s References: 568s >0 568s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 568s /usr/bin/bowtie2 --local --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 568s @HD VN:1.5 SO:unsorted GO:query 568s @SQ SN:0 LN:340 568s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 568s r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 272 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 272 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 272 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s r0 272 0 219 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 568s (fw:1, sam:1) 568s References: 568s >0 568s TTGTTCGTTTGTTCGT 568s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 568s /usr/bin/bowtie2 -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 569s @HD VN:1.5 SO:unsorted GO:query 569s @SQ SN:0 LN:16 569s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 569s r0 0 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 569s r0 256 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 569s (fw:0, sam:1) 569s References: 569s >0 569s TTGTTCGTTTGTTCGT 569s /usr/bin/bowtie2 -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 569s @HD VN:1.5 SO:unsorted GO:query 569s @SQ SN:0 LN:16 569s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 569s r0 16 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 569s r0 272 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 569s (fw:1, sam:1) 569s References: 569s >0 569s TTGTTCGTTTGTTCGT 569s /usr/bin/bowtie2 -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 569s @HD VN:1.5 SO:unsorted GO:query 569s @SQ SN:0 LN:16 569s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 569s r0 4 * 0 0 * * 0 0 TTGTTCAT IIIIIIII YT:Z:UU 569s (fw:0, sam:1) 569s References: 569s >0 569s TTGTTCGTTTGTTCGT 569s /usr/bin/bowtie2 -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 569s @HD VN:1.5 SO:unsorted GO:query 569s @SQ SN:0 LN:16 569s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 569s r0 4 * 0 0 * * 0 0 ATGAACAA IIIIIIII YT:Z:UU 569s (fw:1, sam:1) 569s References: 569s >0 569s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 569s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 570s /usr/bin/bowtie2 --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 570s @HD VN:1.5 SO:unsorted GO:query 570s @SQ SN:0 LN:49 570s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 570s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s (fw:0, sam:1) 570s References: 570s >0 570s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 570s /usr/bin/bowtie2 --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 570s @HD VN:1.5 SO:unsorted GO:query 570s @SQ SN:0 LN:49 570s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 570s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 570s Gap penalties 1 (fw:1, sam:1) 570s References: 570s >0 570s TTGTTCGTTTGTTCGT 570s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 571s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 571s @HD VN:1.5 SO:unsorted GO:query 571s @SQ SN:0 LN:16 571s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 571s r0 0 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU 571s Gap penalties 1 (fw:0, sam:1) 571s References: 571s >0 571s TTGTTCGTTTGTTCGT 571s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 571s @HD VN:1.5 SO:unsorted GO:query 571s @SQ SN:0 LN:16 571s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 571s r0 16 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU 571s Gap penalties 2 (fw:1, sam:1) 571s References: 571s >0 571s TTGTTCGTTTGTTCGT 571s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 571s @HD VN:1.5 SO:unsorted GO:query 571s @SQ SN:0 LN:16 571s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 571s r0 4 * 0 0 * * 0 0 TTGTTCTTTGTT IIIIIIIIIIII YT:Z:UU 571s Gap penalties 2 (fw:0, sam:1) 571s References: 571s >0 571s TTGTTCGTTTGTTCGT 571s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 571s @HD VN:1.5 SO:unsorted GO:query 571s @SQ SN:0 LN:16 571s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 571s r0 4 * 0 0 * * 0 0 AACAAAGAACAA IIIIIIIIIIII YT:Z:UU 571s Gap penalties 3 (fw:1, sam:1) 571s References: 571s >0 571s TTGTTCGTTTGTTCGT 571s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 571s @HD VN:1.5 SO:unsorted GO:query 571s @SQ SN:0 LN:16 571s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 571s r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 571s Gap penalties 3 (fw:0, sam:1) 571s References: 571s >0 571s TTGTTCGTTTGTTCGT 571s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 571s @HD VN:1.5 SO:unsorted GO:query 571s @SQ SN:0 LN:16 571s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 571s r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 571s Gap penalties 4 (fw:1, sam:1) 571s References: 571s >0 571s TTGTTCGTTTGTTCGT 571s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 571s @HD VN:1.5 SO:unsorted GO:query 571s @SQ SN:0 LN:16 571s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 571s r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU 571s Gap penalties 4 (fw:0, sam:1) 571s References: 571s >0 571s TTGTTCGTTTGTTCGT 571s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 571s @HD VN:1.5 SO:unsorted GO:query 571s @SQ SN:0 LN:16 571s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 571s r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU 571s Gap penalties 5 (fw:1, sam:1) 571s References: 571s >0 571s TTGTTCGTTTGTTCGT 571s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 571s @HD VN:1.5 SO:unsorted GO:query 571s @SQ SN:0 LN:16 571s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 571s r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU 571s Gap penalties 5 (fw:0, sam:1) 571s References: 571s >0 571s TTGTTCGTTTGTTCGT 571s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 571s @HD VN:1.5 SO:unsorted GO:query 571s @SQ SN:0 LN:16 571s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 571s r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU 571s Gap penalties 6 (fw:1, sam:1) 571s References: 571s >0 571s ATTGTTCGTTTGTTCGTA 571s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 572s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 572s @HD VN:1.5 SO:unsorted GO:query 572s @SQ SN:0 LN:18 572s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 572s r0 0 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU 572s Gap penalties 6 (fw:0, sam:1) 572s References: 572s >0 572s ATTGTTCGTTTGTTCGTA 572s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 572s @HD VN:1.5 SO:unsorted GO:query 572s @SQ SN:0 LN:18 572s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 572s r0 16 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU 572s Gap penalties 7 (fw:1, sam:1) 572s References: 572s >0 572s TTGTTCGTTTGTTCGT 572s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 572s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 572s @HD VN:1.5 SO:unsorted GO:query 572s @SQ SN:0 LN:16 572s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 572s r0 4 * 0 0 * * 0 0 TTGTTGTTTGATTCGT IIIIIIIIIIIIIIII YT:Z:UU 572s Gap penalties 7 (fw:0, sam:1) 572s References: 572s >0 572s TTGTTCGTTTGTTCGT 572s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 572s @HD VN:1.5 SO:unsorted GO:query 572s @SQ SN:0 LN:16 572s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 572s r0 4 * 0 0 * * 0 0 ACGAATCAAACAACAA IIIIIIIIIIIIIIII YT:Z:UU 572s N filtering 1 (fw:1, sam:1) 572s References: 572s >0 572s GAGACTTTATACGCATCGAACTATCGCTCTA 572s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 573s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 573s @HD VN:1.5 SO:unsorted GO:query 573s @SQ SN:0 LN:31 573s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 573s r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 573s N filtering 1 (fw:0, sam:1) 573s References: 573s >0 573s GAGACTTTATACGCATCGAACTATCGCTCTA 573s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 573s @HD VN:1.5 SO:unsorted GO:query 573s @SQ SN:0 LN:31 573s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 573s r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 573s N filtering 2 (fw:1, sam:1) 573s References: 573s >0 573s GAGACTTTATNCGCATCGAACTATCGCTCTA 573s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 573s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 574s @HD VN:1.5 SO:unsorted GO:query 574s @SQ SN:0 LN:31 574s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 574s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 574s N filtering 2 (fw:0, sam:1) 574s References: 574s >0 574s GAGACTTTATNCGCATCGAACTATCGCTCTA 574s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 574s @HD VN:1.5 SO:unsorted GO:query 574s @SQ SN:0 LN:31 574s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 574s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 574s N filtering 3 (fw:1, sam:1) 574s References: 574s >0 574s GAGACTTTATACGCATCGAANTATCGCTCTA 574s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 574s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 574s @HD VN:1.5 SO:unsorted GO:query 574s @SQ SN:0 LN:31 574s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 574s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 574s N filtering 3 (fw:0, sam:1) 574s References: 574s >0 574s GAGACTTTATACGCATCGAANTATCGCTCTA 574s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 574s @HD VN:1.5 SO:unsorted GO:query 574s @SQ SN:0 LN:31 574s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 574s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 574s N filtering 4 (fw:1, sam:1) 574s References: 574s >0 574s GAGACTTTNTACGCATCGAACTATCGCTCTA 574s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 575s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 575s @HD VN:1.5 SO:unsorted GO:query 575s @SQ SN:0 LN:31 575s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 575s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 575s N filtering 4 (fw:0, sam:1) 575s References: 575s >0 575s GAGACTTTNTACGCATCGAACTATCGCTCTA 575s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 575s @HD VN:1.5 SO:unsorted GO:query 575s @SQ SN:0 LN:31 575s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 575s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 575s N filtering 5 (fw:1, sam:1) 575s References: 575s >0 575s GAGACTTTATNCGCATCGAACTATCGCTCTA 575s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 575s /usr/bin/bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 575s @HD VN:1.5 SO:unsorted GO:query 575s @SQ SN:0 LN:31 575s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 575s r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU 575s N filtering 5 (fw:0, sam:1) 575s References: 575s >0 575s GAGACTTTATNCGCATCGAACTATCGCTCTA 575s /usr/bin/bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 575s @HD VN:1.5 SO:unsorted GO:query 575s @SQ SN:0 LN:31 575s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 575s r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU 575s N filtering 6 (fw:1, sam:1) 575s References: 575s >0 575s GAGACTTTNTACGCATCGAANTATCGCTCTA 575s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 576s /usr/bin/bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 576s @HD VN:1.5 SO:unsorted GO:query 576s @SQ SN:0 LN:31 576s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 576s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 576s N filtering 6 (fw:0, sam:1) 576s References: 576s >0 576s GAGACTTTNTACGCATCGAANTATCGCTCTA 576s /usr/bin/bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 576s @HD VN:1.5 SO:unsorted GO:query 576s @SQ SN:0 LN:31 576s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 576s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 576s (fw:1, sam:1) 576s References: 576s >0 576s TTTTGTTCGTTTG 576s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 576s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 577s @HD VN:1.5 SO:unsorted GO:query 577s @SQ SN:0 LN:13 577s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 577s r0 0 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 577s (fw:0, sam:1) 577s References: 577s >0 577s TTTTGTTCGTTTG 577s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 577s @HD VN:1.5 SO:unsorted GO:query 577s @SQ SN:0 LN:13 577s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 577s r0 16 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 577s (fw:1, sam:1) 577s References: 577s >0 577s TTGTTCGTTTGTT 577s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 577s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 577s @HD VN:1.5 SO:unsorted GO:query 577s @SQ SN:0 LN:13 577s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 577s r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 577s (fw:0, sam:1) 577s References: 577s >0 577s TTGTTCGTTTGTT 577s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 577s @HD VN:1.5 SO:unsorted GO:query 577s @SQ SN:0 LN:13 577s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 577s r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 577s (fw:1, sam:1) 577s References: 577s >0 577s ACNCA 577s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 578s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 578s @HD VN:1.5 SO:unsorted GO:query 578s @SQ SN:0 LN:5 578s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 578s r0 0 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 578s (fw:0, sam:1) 578s References: 578s >0 578s ACNCA 578s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 578s @HD VN:1.5 SO:unsorted GO:query 578s @SQ SN:0 LN:5 578s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 578s r0 16 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 578s N ceil = 0, 2 legit hits (1) (fw:1, sam:1) 578s References: 578s >0 578s ACNCA 578s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 578s @HD VN:1.5 SO:unsorted GO:query 578s @SQ SN:0 LN:5 578s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 578s r0 0 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 578s N ceil = 0, 2 legit hits (1) (fw:0, sam:1) 578s References: 578s >0 578s ACNCA 578s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 578s @HD VN:1.5 SO:unsorted GO:query 578s @SQ SN:0 LN:5 578s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 578s r0 16 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 578s N ceil = 0, 2 legit hits (2) (fw:1, sam:1) 578s References: 578s >0 578s ACNCANNNNNNNNCGNNNNNNNNCG 578s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 578s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 579s @HD VN:1.5 SO:unsorted GO:query 579s @SQ SN:0 LN:25 579s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 579s r0 0 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s N ceil = 0, 2 legit hits (2) (fw:0, sam:1) 579s References: 579s >0 579s ACNCANNNNNNNNCGNNNNNNNNCG 579s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 579s @HD VN:1.5 SO:unsorted GO:query 579s @SQ SN:0 LN:25 579s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 579s r0 0 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s (fw:1, sam:1) 579s References: 579s >0 579s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 579s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 579s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 579s @HD VN:1.5 SO:unsorted GO:query 579s @SQ SN:0 LN:37 579s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 579s r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 272 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s (fw:0, sam:1) 579s References: 579s >0 579s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 579s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 579s @HD VN:1.5 SO:unsorted GO:query 579s @SQ SN:0 LN:37 579s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 579s r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 272 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s (fw:1, sam:1) 579s References: 579s >0 579s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 579s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 579s @HD VN:1.5 SO:unsorted GO:query 579s @SQ SN:0 LN:37 579s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 579s r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 272 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s (fw:0, sam:1) 579s References: 579s >0 579s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 579s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 579s @HD VN:1.5 SO:unsorted GO:query 579s @SQ SN:0 LN:37 579s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 579s r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 272 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 579s (fw:1, sam:1) 579s References: 579s >0 579s TTGTTYGT 579s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 580s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 580s @HD VN:1.5 SO:unsorted GO:query 580s @SQ SN:0 LN:8 580s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 580s r0 0 0 1 255 8M * 0 0 TTGTTGGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU 580s r1 0 0 1 255 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU 580s (fw:1, sam:1) 580s References: 580s >0 580s ATAACCTTCG 580s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 580s /usr/bin/bowtie2 --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 580s @HD VN:1.5 SO:unsorted GO:query 580s @SQ SN:0 LN:10 580s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 580s r0 0 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU 580s (fw:0, sam:1) 580s References: 580s >0 580s ATAACCTTCG 580s /usr/bin/bowtie2 --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 580s @HD VN:1.5 SO:unsorted GO:query 580s @SQ SN:0 LN:10 580s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 580s r0 16 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU 580s (fw:1, sam:1) 580s References: 580s >0 580s ATATGCCCCATGCCCCCCTCCG 580s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 580s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 580s @HD VN:1.5 SO:unsorted GO:query 580s @SQ SN:0 LN:22 580s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 580s r0 0 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU 580s (fw:1, sam:1) 580s References: 580s >0 580s ATATGCCCCATGCCCCCCTCCG 580s /usr/bin/bowtie2 --quiet -a --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 581s @HD VN:1.5 SO:unsorted GO:query 581s @SQ SN:0 LN:22 581s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 581s r0 16 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU 581s Simple paired-end 13 (fw:1, sam:1) 581s References: 581s >0 581s TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC 581s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 581s /usr/bin/bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz 581s @HD VN:1.5 SO:unsorted GO:query 581s @SQ SN:0 LN:51 581s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" 581s r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r0 129 0 31 255 10M = 4 -37 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r1 65 0 4 255 10M = 30 36 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r1 129 0 30 255 10M = 4 -36 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r2 67 0 4 255 10M = 29 35 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r2 131 0 29 255 10M = 4 -35 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r3 67 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r3 131 0 28 255 10M = 4 -34 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r4 65 0 5 255 10M = 31 36 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r4 129 0 31 255 10M = 5 -36 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r5 67 0 5 255 10M = 30 35 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r5 131 0 30 255 10M = 5 -35 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r6 67 0 5 255 10M = 29 34 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r6 131 0 29 255 10M = 5 -34 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r7 67 0 5 255 10M = 28 33 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r7 131 0 28 255 10M = 5 -33 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s Simple paired-end 13 (fw:0, sam:1) 581s References: 581s >0 581s TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC 581s /usr/bin/bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz 581s @HD VN:1.5 SO:unsorted GO:query 581s @SQ SN:0 LN:51 581s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" 581s r0 113 0 31 255 10M = 4 -37 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r1 113 0 30 255 10M = 4 -36 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r1 177 0 4 255 10M = 30 36 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r2 115 0 29 255 10M = 4 -35 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r2 179 0 4 255 10M = 29 35 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r3 115 0 28 255 10M = 4 -34 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r3 179 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r4 113 0 31 255 10M = 5 -36 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r4 177 0 5 255 10M = 31 36 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r5 115 0 30 255 10M = 5 -35 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r5 179 0 5 255 10M = 30 35 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r6 115 0 29 255 10M = 5 -34 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r6 179 0 5 255 10M = 29 34 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r7 115 0 28 255 10M = 5 -33 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r7 179 0 5 255 10M = 28 33 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s Simple paired-end 12 (fw:1, sam:1) 581s References: 581s >0 581s TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC 581s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 581s /usr/bin/bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 581s @HD VN:1.5 SO:unsorted GO:query 581s @SQ SN:0 LN:51 581s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 581s r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r0 129 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r1 67 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r1 131 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s Simple paired-end 12 (fw:0, sam:1) 581s References: 581s >0 581s TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC 581s /usr/bin/bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 581s @HD VN:1.5 SO:unsorted GO:query 581s @SQ SN:0 LN:51 581s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 581s r0 113 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 581s r1 115 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s r1 179 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 581s Simple paired-end 11 (fw:1, sam:1) 581s References: 581s >0 581s TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC 581s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 582s /usr/bin/bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 582s @HD VN:1.5 SO:unsorted GO:query 582s @SQ SN:0 LN:51 582s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 582s r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 582s r0 129 0 31 255 10M = 4 -37 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 582s Simple paired-end 11 (fw:0, sam:1) 582s References: 582s >0 582s TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC 582s /usr/bin/bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 582s @HD VN:1.5 SO:unsorted GO:query 582s @SQ SN:0 LN:51 582s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 582s r0 113 0 31 255 10M = 4 -37 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 582s r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 582s Simple paired-end 10 (fw:1, sam:1) 582s References: 582s >0 582s TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC 582s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 582s /usr/bin/bowtie2 -I 28 -X 80 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 582s @HD VN:1.5 SO:unsorted GO:query 582s @SQ SN:0 LN:41 582s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 582s r0 65 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 582s r0 129 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 582s Simple paired-end 10 (fw:0, sam:1) 582s References: 582s >0 582s TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC 582s /usr/bin/bowtie2 -I 28 -X 80 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 582s @HD VN:1.5 SO:unsorted GO:query 582s @SQ SN:0 LN:41 582s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 582s r0 113 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 582s r0 177 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 582s Simple paired-end 9 (fw:1, sam:1) 582s References: 582s >0 582s CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC 582s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 582s /usr/bin/bowtie2 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 582s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 582s @HD VN:1.5 SO:unsorted GO:query 582s @SQ SN:0 LN:81 582s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 582s r0 99 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s r0 147 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s Simple paired-end 9 (fw:0, sam:1) 582s References: 582s >0 582s CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC 582s /usr/bin/bowtie2 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 582s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 582s @HD VN:1.5 SO:unsorted GO:query 582s @SQ SN:0 LN:81 582s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 582s r0 83 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s r0 163 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s Simple paired-end 8 (fw:1, sam:1) 582s References: 582s >0 582s CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC 582s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 582s /usr/bin/bowtie2 -I 0 -X 80 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 582s @HD VN:1.5 SO:unsorted GO:query 582s @SQ SN:0 LN:81 582s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 582s r0 99 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s r0 147 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s r0 355 0 4 255 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s r0 403 0 60 255 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s r0 355 0 38 255 10M = 60 32 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s r0 403 0 60 255 10M = 38 -32 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s Simple paired-end 8 (fw:0, sam:1) 582s References: 582s >0 582s CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC 582s /usr/bin/bowtie2 -I 0 -X 80 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 582s @HD VN:1.5 SO:unsorted GO:query 582s @SQ SN:0 LN:81 582s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 582s r0 83 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s r0 163 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s r0 339 0 60 255 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s r0 419 0 4 255 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s r0 339 0 60 255 10M = 38 -32 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 582s r0 419 0 38 255 10M = 60 32 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 583s Simple paired-end 2; no --no-mixed (fw:0, sam:1) 583s References: 583s >0 583s CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC 583s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 583s /usr/bin/bowtie2 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 583s @HD VN:1.5 SO:unsorted GO:query 583s @SQ SN:0 LN:53 583s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 583s r0 153 0 4 255 10M = 4 0 ATATATATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UP 583s r0 101 0 4 0 * = 4 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 583s Simple paired-end 2; --no-mixed (fw:1, sam:1) 583s References: 583s >0 583s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC 583s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 583s /usr/bin/bowtie2 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 583s @HD VN:1.5 SO:unsorted GO:query 583s @SQ SN:0 LN:53 583s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 583s r0 77 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP 583s r0 141 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 583s Simple paired-end 2; --no-mixed (fw:0, sam:1) 583s References: 583s >0 583s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC 583s /usr/bin/bowtie2 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 583s @HD VN:1.5 SO:unsorted GO:query 583s @SQ SN:0 LN:53 583s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 583s r0 77 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 583s r0 141 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP 583s Simple paired-end 1 (fw:1, sam:1) 583s References: 583s >0 583s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC 583s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 584s /usr/bin/bowtie2 -I 0 -X 50 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 584s @HD VN:1.5 SO:unsorted GO:query 584s @SQ SN:0 LN:53 584s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 584s r0 67 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 584s r0 131 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 584s Simple paired-end 1 (fw:0, sam:1) 584s References: 584s >0 584s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC 584s /usr/bin/bowtie2 -I 0 -X 50 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 584s @HD VN:1.5 SO:unsorted GO:query 584s @SQ SN:0 LN:53 584s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 584s r0 115 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 584s r0 179 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 584s (fw:1, sam:1) 584s References: 584s >0 584s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 584s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 584s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 584s @HD VN:1.5 SO:unsorted GO:query 584s @SQ SN:0 LN:49 584s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 584s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s (fw:0, sam:1) 584s References: 584s >0 584s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 584s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 584s @HD VN:1.5 SO:unsorted GO:query 584s @SQ SN:0 LN:49 584s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 584s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 584s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 585s (fw:1, sam:1) 585s References: 585s >0 585s TTGTTCGTTTGTTCGT 585s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 585s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 585s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 585s @HD VN:1.5 SO:unsorted GO:query 585s @SQ SN:0 LN:16 585s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 585s r0 0 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 585s (fw:0, sam:1) 585s References: 585s >0 585s TTGTTCGTTTGTTCGT 585s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 585s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 585s @HD VN:1.5 SO:unsorted GO:query 585s @SQ SN:0 LN:16 585s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 585s r0 16 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 585s (fw:1, sam:1) 585s References: 585s >0 585s TTGTTCGT 585s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 585s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 586s @HD VN:1.5 SO:unsorted GO:query 586s @SQ SN:0 LN:8 586s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 586s r0 0 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 586s (fw:0, sam:1) 586s References: 586s >0 586s TTGTTCGT 586s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 586s @HD VN:1.5 SO:unsorted GO:query 586s @SQ SN:0 LN:8 586s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 586s r0 16 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 586s (fw:1, sam:1) 586s References: 586s >0 586s TTGTTCGTTTGTTCGT 586s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 586s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 586s @HD VN:1.5 SO:unsorted GO:query 586s @SQ SN:0 LN:16 586s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 586s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 586s (fw:0, sam:1) 586s References: 586s >0 586s TTGTTCGTTTGTTCGT 586s /usr/bin/bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 586s @HD VN:1.5 SO:unsorted GO:query 586s @SQ SN:0 LN:16 586s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 586s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 586s (fw:1, sam:1) 586s References: 586s >0 586s TTGTTCGTTTGTTCGT 586s /usr/bin/bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 586s @HD VN:1.5 SO:unsorted GO:query 586s @SQ SN:0 LN:16 586s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 586s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 586s (fw:0, sam:1) 586s References: 586s >0 586s TTGTTCGTTTGTTCGT 586s /usr/bin/bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 586s @HD VN:1.5 SO:unsorted GO:query 586s @SQ SN:0 LN:16 586s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 586s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 586s (fw:1, sam:1) 586s References: 586s >0 586s TTGTTCGTTTGTTCGT 586s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 586s @HD VN:1.5 SO:unsorted GO:query 586s @SQ SN:0 LN:16 586s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 586s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 586s (fw:0, sam:1) 586s References: 586s >0 586s TTGTTCGTTTGTTCGT 586s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 586s @HD VN:1.5 SO:unsorted GO:query 586s @SQ SN:0 LN:16 586s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 586s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 586s (fw:1, sam:1) 586s References: 586s >0 586s TTGTTCGTTTGTTCGT 586s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 586s @HD VN:1.5 SO:unsorted GO:query 586s @SQ SN:0 LN:16 586s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 586s r0 0 0 9 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 586s r0 256 0 1 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 586s r0 256 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU 586s r0 256 0 4 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2C0G1T0T0G0 YT:Z:UU 586s r0 256 0 8 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T0G1T0C0G0 YT:Z:UU 586s r0 256 0 6 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:0C0G0T2G0T1 YT:Z:UU 586s (fw:0, sam:1) 586s References: 586s >0 586s TTGTTCGTTTGTTCGT 586s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 587s @HD VN:1.5 SO:unsorted GO:query 587s @SQ SN:0 LN:16 587s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 587s r0 16 0 1 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 587s r0 272 0 9 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 587s r0 272 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU 587s r0 272 0 6 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:0C0G0T2G0T1 YT:Z:UU 587s r0 272 0 4 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2C0G1T0T0G0 YT:Z:UU 587s r0 272 0 8 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T0G1T0C0G0 YT:Z:UU 587s FASTA-continuous 1 (fw:1, sam:1) 587s References: 587s >0 587s AGCATCGATCAGTATCTGA 587s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 587s /usr/bin/bowtie2 --large-index -F 10,9 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp .simple_tests.gz 587s @HD VN:1.5 SO:unsorted GO:query 587s @SQ SN:0 LN:19 587s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp .simple_tests.gz" 587s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 587s seq1_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 587s FASTA-continuous 2 (fw:1, sam:1) 587s References: 587s >0 587s AGCATCGATCAGTATCTGA 587s /usr/bin/bowtie2 --large-index -F 10,9 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp .simple_tests.gz 587s @HD VN:1.5 SO:unsorted GO:query 587s @SQ SN:0 LN:19 587s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp .simple_tests.gz" 587s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 587s seq2_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 587s seq2_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 587s FASTA-continuous 3 (fw:1, sam:1) 587s References: 587s >0 587s AGCATCGATCAGTATCTGA 587s /usr/bin/bowtie2 --large-index -F 10,9 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz 587s @HD VN:1.5 SO:unsorted GO:query 587s @SQ SN:0 LN:19 587s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz" 587s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 587s FASTA-continuous 4 (fw:1, sam:1) 587s References: 587s >0 587s AGCATCGATCAGTATCTGA 587s /usr/bin/bowtie2 --large-index -F 10,9 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp .simple_tests.gz 587s @HD VN:1.5 SO:unsorted GO:query 587s @SQ SN:0 LN:19 587s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp .simple_tests.gz" 587s seq1_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 587s FASTA-continuous 5 (fw:1, sam:1) 587s References: 587s >0 587s AGCATCGATCAGTATCTGA 587s /usr/bin/bowtie2 --large-index -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz 587s @HD VN:1.5 SO:unsorted GO:query 587s @SQ SN:0 LN:19 587s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz" 587s seq2_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 587s FASTA-continuous 6 (fw:1, sam:1) 587s References: 587s >0 587s AGCATCGATCAG 587s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 587s /usr/bin/bowtie2 --large-index -F 10,1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz 588s @HD VN:1.5 SO:unsorted GO:query 588s @SQ SN:0 LN:12 588s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz" 588s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 588s seq1_1 0 0 2 255 10M * 0 0 GCATCGATCA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 588s seq1_2 0 0 3 255 10M * 0 0 CATCGATCAG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 588s Align should not fail when first seq in ref is all Ns (fw:1, sam:1) 588s References: 588s >0 588s NNNNNNNNNNNNNNN 588s >1 588s AGCATCGATCAGTATCTGA 588s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 588s Warning: Encountered reference sequence with only gaps 588s Warning: Encountered reference sequence with only gaps 588s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG 588s @HD VN:1.5 SO:unsorted GO:query 588s @SQ SN:0 LN:15 588s @SQ SN:1 LN:19 588s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 588s 0 0 1 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 588s Align should not fail when multiple seqs are all Ns (fw:1, sam:1) 588s References: 588s >0 588s NNNNNNNNNNNNNNN 588s >1 588s NNNNNNNNNNNNNNN 588s >2 588s AGCATCGATCAGTATCTGA 588s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 588s Warning: Encountered reference sequence with only gaps 588s Warning: Encountered reference sequence with only gaps 588s Warning: Encountered reference sequence with only gaps 588s Warning: Encountered reference sequence with only gaps 588s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG 589s @HD VN:1.5 SO:unsorted GO:query 589s @SQ SN:0 LN:15 589s @SQ SN:1 LN:15 589s @SQ SN:2 LN:19 589s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 589s 0 0 2 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 589s Should account for stretch of Ns at beginning (fw:1, sam:1) 589s References: 589s >0 589s NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA 589s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 589s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG 589s @HD VN:1.5 SO:unsorted GO:query 589s @SQ SN:0 LN:34 589s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 589s 0 0 0 18 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 589s Cline 1 (fw:1, sam:1) 589s References: 589s >0 589s AGCATCGATCAGTATCTGA 589s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 589s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG 589s @HD VN:1.5 SO:unsorted GO:query 589s @SQ SN:0 LN:19 589s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 589s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 589s Cline 2 (fw:1, sam:1) 589s References: 589s >0 589s AGCATCGATCAGTATCTGA 589s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 589s @HD VN:1.5 SO:unsorted GO:query 589s @SQ SN:0 LN:19 589s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 589s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 589s Cline 2 (fw:1, sam:1) 589s References: 589s >0 589s AGCATCGATCAGTATCTGA 589s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP 589s @HD VN:1.5 SO:unsorted GO:query 589s @SQ SN:0 LN:19 589s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" 589s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG ABCDEDGHIJKLMNOP AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 589s Cline 4 (fw:1, sam:1) 589s References: 589s >0 589s AGCATCGATCAGTATCTGA 589s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO 589s Error: Read 0 has more read characters than quality values. 589s terminate called after throwing an instance of 'int' 590s Aborted (core dumped) 590s (ERR): bowtie2-align exited with value 134 590s Cline 5 (fw:1, sam:1) 590s References: 590s >0 590s AGCATCGATCAGTATCTGA 590s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ 590s Error: Read 0 has more quality values than read characters. 590s terminate called after throwing an instance of 'int' 590s Aborted (core dumped) 590s (ERR): bowtie2-align exited with value 134 590s trim-to: trim from 5'-end (fw:1, sam:1) 590s References: 590s >0 590s AGCATCGATCAGTATCTGA 590s /usr/bin/bowtie2 --large-index --trim-to 5:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 590s 590s @HD VN:1.5 SO:unsorted GO:query 590s @SQ SN:0 LN:19 590s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 590s 0 0 0 7 255 12M * 0 0 GATCAGTATCTG IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 590s trim-to: trim from 3'-end (fw:1, sam:1) 590s References: 590s >0 590s AGCATCGATCAGTATCTGA 590s /usr/bin/bowtie2 --large-index --trim-to 3:12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 590s 590s @HD VN:1.5 SO:unsorted GO:query 590s @SQ SN:0 LN:19 590s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 590s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 590s trim-to: trim from 3'-end (default) (fw:1, sam:1) 590s References: 590s >0 590s AGCATCGATCAGTATCTGA 590s /usr/bin/bowtie2 --large-index --trim-to 12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 590s 590s @HD VN:1.5 SO:unsorted GO:query 590s @SQ SN:0 LN:19 590s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 590s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 590s trim-to: invalid position (fw:1, sam:1) 590s References: 590s >0 590s AGCATCGATCAGTATCTGA 590s /usr/bin/bowtie2 --large-index --trim-to 4:12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 590s 590s --trim-to: trim position must be either 3 or 5 590s Bowtie 2 version 2.5.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 590s Usage: 590s bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] 590s 590s Index filename prefix (minus trailing .X.bt2l). 590s NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. 590s Files with #1 mates, paired with files in . 590s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 590s Files with #2 mates, paired with files in . 590s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 590s Files with unpaired reads. 590s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 590s Files with interleaved paired-end FASTQ/FASTA reads 590s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 590s Files are unaligned BAM sorted by read name. 590s File for SAM output (default: stdout) 590s 590s , , can be comma-separated lists (no whitespace) and can be 590s specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 590s 590s Options (defaults in parentheses): 590s 590s Input: 590s -q query input files are FASTQ .fq/.fastq (default) 590s --tab5 query input files are TAB5 .tab5 590s --tab6 query input files are TAB6 .tab6 590s --qseq query input files are in Illumina's qseq format 590s -f query input files are (multi-)FASTA .fa/.mfa 590s -r query input files are raw one-sequence-per-line 590s -F k:,i: query input files are continuous FASTA where reads 590s are substrings (k-mers) extracted from a FASTA file 590s and aligned at offsets 1, 1+i, 1+2i ... end of reference 590s -c , , are sequences themselves, not files 590s -s/--skip skip the first reads/pairs in the input (none) 590s -u/--upto stop after first reads/pairs (no limit) 590s -5/--trim5 trim bases from 5'/left end of reads (0) 590s -3/--trim3 trim bases from 3'/right end of reads (0) 590s --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end 590s If the read end is not specified then it defaults to 3 (0) 590s --phred33 qualities are Phred+33 (default) 590s --phred64 qualities are Phred+64 590s --int-quals qualities encoded as space-delimited integers 590s 590s Presets: Same as: 590s For --end-to-end: 590s --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 590s --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 590s --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default) 590s --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 590s 590s For --local: 590s --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 590s --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 590s --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) 590s --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 590s 590s Alignment: 590s -N max # mismatches in seed alignment; can be 0 or 1 (0) 590s -L length of seed substrings; must be >3, <32 (22) 590s -i interval between seed substrings w/r/t read len (S,1,1.15) 590s --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) 590s --dpad include extra ref chars on sides of DP table (15) 590s --gbar disallow gaps within nucs of read extremes (4) 590s --ignore-quals treat all quality values as 30 on Phred scale (off) 590s --nofw do not align forward (original) version of read (off) 590s --norc do not align reverse-complement version of read (off) 590s --no-1mm-upfront do not allow 1 mismatch alignments before attempting to 590s scan for the optimal seeded alignments 590s --end-to-end entire read must align; no clipping (on) 590s OR 590s --local local alignment; ends might be soft clipped (off) 590s 590s Scoring: 590s --ma match bonus (0 for --end-to-end, 2 for --local) 590s --mp max penalty for mismatch; lower qual = lower penalty (6) 590s --np penalty for non-A/C/G/Ts in read/ref (1) 590s --rdg , read gap open, extend penalties (5,3) 590s --rfg , reference gap open, extend penalties (5,3) 590s --score-min min acceptable alignment score w/r/t read length 590s (G,20,8 for local, L,-0.6,-0.6 for end-to-end) 590s 590s Reporting: 590s (default) look for multiple alignments, report best, with MAPQ 590s OR 590s -k report up to alns per read; MAPQ not meaningful 590s OR 590s -a/--all report all alignments; very slow, MAPQ not meaningful 590s 590s Effort: 590s -D give up extending after failed extends in a row (15) 590s -R for reads w/ repetitive seeds, try sets of seeds (2) 590s 590s Paired-end: 590s -I/--minins minimum fragment length (0) 590s -X/--maxins maximum fragment length (500) 590s --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) 590s --no-mixed suppress unpaired alignments for paired reads 590s --no-discordant suppress discordant alignments for paired reads 590s --dovetail concordant when mates extend past each other 590s --no-contain not concordant when one mate alignment contains other 590s --no-overlap not concordant when mates overlap at all 590s 590s BAM: 590s --align-paired-reads 590s Bowtie2 will, by default, attempt to align unpaired BAM reads. 590s Use this option to align paired-end reads instead. 590s --preserve-tags Preserve tags from the original BAM record by 590s appending them to the end of the corresponding SAM output. 590s 590s Output: 590s -t/--time print wall-clock time taken by search phases 590s --un write unpaired reads that didn't align to 590s --al write unpaired reads that aligned at least once to 590s --un-conc write pairs that didn't align concordantly to 590s --al-conc write pairs that aligned concordantly at least once to 590s (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. 590s --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) 590s --quiet print nothing to stderr except serious errors 590s --met-file send metrics to file at (off) 590s --met-stderr send metrics to stderr (off) 590s --met report internal counters & metrics every secs (1) 590s --no-unal suppress SAM records for unaligned reads 590s --no-head suppress header lines, i.e. lines starting with @ 590s --no-sq suppress @SQ header lines 590s --rg-id set read group id, reflected in @RG line and RG:Z: opt field 590s --rg add ("lab:value") to @RG line of SAM header. 590s Note: @RG line only printed when --rg-id is set. 590s --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments. 590s --sam-no-qname-trunc 590s Suppress standard behavior of truncating readname at first whitespace 590s at the expense of generating non-standard SAM. 590s --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record. 590s --soft-clipped-unmapped-tlen 590s Exclude soft-clipped bases when reporting TLEN 590s --sam-append-comment 590s Append FASTA/FASTQ comment to SAM record 590s 590s Performance: 590s -p/--threads number of alignment threads to launch (1) 590s --reorder force SAM output order to match order of input reads 590s --mm use memory-mapped I/O for index; many 'bowtie's can share 590s 590s Other: 590s --qc-filter filter out reads that are bad according to QSEQ filter 590s --seed seed for random number generator (0) 590s --non-deterministic 590s seed rand. gen. arbitrarily instead of using read attributes 590s --version print version information and quit 590s -h/--help print this usage message 590s Error: Encountered internal Bowtie 2 exception (#1) 590s Command: /usr/bin/bowtie2-align-l --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 590s (ERR): bowtie2-align exited with value 1 591s trim-to: invalid count (fw:1, sam:1) 591s References: 591s >0 591s AGCATCGATCAGTATCTGA 591s /usr/bin/bowtie2 --large-index --trim-to 5:-12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 591s 591s --trim-to: the number bases to trim must be at least 0 591s Bowtie 2 version 2.5.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 591s Usage: 591s bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] 591s 591s Index filename prefix (minus trailing .X.bt2l). 591s NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. 591s Files with #1 mates, paired with files in . 591s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 591s Files with #2 mates, paired with files in . 591s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 591s Files with unpaired reads. 591s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 591s Files with interleaved paired-end FASTQ/FASTA reads 591s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 591s Files are unaligned BAM sorted by read name. 591s File for SAM output (default: stdout) 591s 591s , , can be comma-separated lists (no whitespace) and can be 591s specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 591s 591s Options (defaults in parentheses): 591s 591s Input: 591s -q query input files are FASTQ .fq/.fastq (default) 591s --tab5 query input files are TAB5 .tab5 591s --tab6 query input files are TAB6 .tab6 591s --qseq query input files are in Illumina's qseq format 591s -f query input files are (multi-)FASTA .fa/.mfa 591s -r query input files are raw one-sequence-per-line 591s -F k:,i: query input files are continuous FASTA where reads 591s are substrings (k-mers) extracted from a FASTA file 591s and aligned at offsets 1, 1+i, 1+2i ... end of reference 591s -c , , are sequences themselves, not files 591s -s/--skip skip the first reads/pairs in the input (none) 591s -u/--upto stop after first reads/pairs (no limit) 591s -5/--trim5 trim bases from 5'/left end of reads (0) 591s -3/--trim3 trim bases from 3'/right end of reads (0) 591s --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end 591s If the read end is not specified then it defaults to 3 (0) 591s --phred33 qualities are Phred+33 (default) 591s --phred64 qualities are Phred+64 591s --int-quals qualities encoded as space-delimited integers 591s 591s Presets: Same as: 591s For --end-to-end: 591s --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 591s --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 591s --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default) 591s --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 591s 591s For --local: 591s --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 591s --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 591s --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) 591s --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 591s 591s Alignment: 591s -N max # mismatches in seed alignment; can be 0 or 1 (0) 591s -L length of seed substrings; must be >3, <32 (22) 591s -i interval between seed substrings w/r/t read len (S,1,1.15) 591s --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) 591s --dpad include extra ref chars on sides of DP table (15) 591s --gbar disallow gaps within nucs of read extremes (4) 591s --ignore-quals treat all quality values as 30 on Phred scale (off) 591s --nofw do not align forward (original) version of read (off) 591s --norc do not align reverse-complement version of read (off) 591s --no-1mm-upfront do not allow 1 mismatch alignments before attempting to 591s scan for the optimal seeded alignments 591s --end-to-end entire read must align; no clipping (on) 591s OR 591s --local local alignment; ends might be soft clipped (off) 591s 591s Scoring: 591s --ma match bonus (0 for --end-to-end, 2 for --local) 591s --mp max penalty for mismatch; lower qual = lower penalty (6) 591s --np penalty for non-A/C/G/Ts in read/ref (1) 591s --rdg , read gap open, extend penalties (5,3) 591s --rfg , reference gap open, extend penalties (5,3) 591s --score-min min acceptable alignment score w/r/t read length 591s (G,20,8 for local, L,-0.6,-0.6 for end-to-end) 591s 591s Reporting: 591s (default) look for multiple alignments, report best, with MAPQ 591s OR 591s -k report up to alns per read; MAPQ not meaningful 591s OR 591s -a/--all report all alignments; very slow, MAPQ not meaningful 591s 591s Effort: 591s -D give up extending after failed extends in a row (15) 591s -R for reads w/ repetitive seeds, try sets of seeds (2) 591s 591s Paired-end: 591s -I/--minins minimum fragment length (0) 591s -X/--maxins maximum fragment length (500) 591s --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) 591s --no-mixed suppress unpaired alignments for paired reads 591s --no-discordant suppress discordant alignments for paired reads 591s --dovetail concordant when mates extend past each other 591s --no-contain not concordant when one mate alignment contains other 591s --no-overlap not concordant when mates overlap at all 591s 591s BAM: 591s --align-paired-reads 591s Bowtie2 will, by default, attempt to align unpaired BAM reads. 591s Use this option to align paired-end reads instead. 591s --preserve-tags Preserve tags from the original BAM record by 591s appending them to the end of the corresponding SAM output. 591s 591s Output: 591s -t/--time print wall-clock time taken by search phases 591s --un write unpaired reads that didn't align to 591s --al write unpaired reads that aligned at least once to 591s --un-conc write pairs that didn't align concordantly to 591s --al-conc write pairs that aligned concordantly at least once to 591s (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. 591s --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) 591s --quiet print nothing to stderr except serious errors 591s --met-file send metrics to file at (off) 591s --met-stderr send metrics to stderr (off) 591s --met report internal counters & metrics every secs (1) 591s --no-unal suppress SAM records for unaligned reads 591s --no-head suppress header lines, i.e. lines starting with @ 591s --no-sq suppress @SQ header lines 591s --rg-id set read group id, reflected in @RG line and RG:Z: opt field 591s --rg add ("lab:value") to @RG line of SAM header. 591s Note: @RG line only printed when --rg-id is set. 591s --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments. 591s --sam-no-qname-trunc 591s Suppress standard behavior of truncating readname at first whitespace 591s at the expense of generating non-standard SAM. 591s --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record. 591s --soft-clipped-unmapped-tlen 591s Exclude soft-clipped bases when reporting TLEN 591s --sam-append-comment 591s Append FASTA/FASTQ comment to SAM record 591s 591s Performance: 591s -p/--threads number of alignment threads to launch (1) 591s --reorder force SAM output order to match order of input reads 591s --mm use memory-mapped I/O for index; many 'bowtie's can share 591s 591s Other: 591s --qc-filter filter out reads that are bad according to QSEQ filter 591s --seed seed for random number generator (0) 591s --non-deterministic 591s seed rand. gen. arbitrarily instead of using read attributes 591s --version print version information and quit 591s -h/--help print this usage message 591s Error: Encountered internal Bowtie 2 exception (#1) 591s Command: /usr/bin/bowtie2-align-l --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 591s (ERR): bowtie2-align exited with value 1 591s Cline 7 (fw:1, sam:1) 591s References: 591s >0 591s AGCATCGATCAGTATCTGA 591s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 591s 591s @HD VN:1.5 SO:unsorted GO:query 591s @SQ SN:0 LN:19 591s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 591s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 591s Cline 8 (fw:1, sam:1) 591s References: 591s >0 591s AGCATCGATCAGTATCTGA 591s /usr/bin/bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 591s @HD VN:1.5 SO:unsorted GO:query 591s @SQ SN:0 LN:19 591s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 591s 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 591s Cline 9 (fw:1, sam:1) 591s References: 591s >0 591s AGCATCGATCAGTATCTGA 591s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 591s @HD VN:1.5 SO:unsorted GO:query 591s @SQ SN:0 LN:19 591s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 591s Cline multiread 1 (fw:1, sam:1) 591s References: 591s >0 591s AGCATCGATCAGTATCTGA 591s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII 591s 591s 591s @HD VN:1.5 SO:unsorted GO:query 591s @SQ SN:0 LN:19 591s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 591s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 591s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 591s Cline multiread 2 (fw:1, sam:1) 591s References: 591s >0 591s AGCATCGATCAGTATCTGA 591s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII 591s 591s 591s @HD VN:1.5 SO:unsorted GO:query 591s @SQ SN:0 LN:19 591s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 591s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 591s Cline multiread 3 (fw:1, sam:1) 591s References: 591s >0 591s AGCATCGATCAGTATCTGA 591s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG 591s 591s @HD VN:1.5 SO:unsorted GO:query 591s @SQ SN:0 LN:19 591s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" 591s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 591s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 591s Cline paired 1 (fw:1, sam:1) 591s References: 591s >0 591s AGCATCGATCAAAAACTGA 591s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 591s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII 592s @HD VN:1.5 SO:unsorted GO:query 592s @SQ SN:0 LN:19 592s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII" 592s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 592s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 592s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 592s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 592s Cline paired 2 (fw:1, sam:1) 592s References: 592s >0 592s AGCATCGATCAAAAACTGA 592s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII 592s @HD VN:1.5 SO:unsorted GO:query 592s @SQ SN:0 LN:19 592s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 592s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 592s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 592s Cline paired 3 (fw:1, sam:1) 592s References: 592s >0 592s AGCATCGATCAAAAACTGA 592s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII 592s @HD VN:1.5 SO:unsorted GO:query 592s @SQ SN:0 LN:19 592s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 592s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 592s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 592s Cline paired 4 (fw:1, sam:1) 592s References: 592s >0 592s AGCATCGATCAAAAACTGA 592s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII 592s @HD VN:1.5 SO:unsorted GO:query 592s @SQ SN:0 LN:19 592s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" 592s 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 592s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 592s Fastq 1 (fw:1, sam:1) 592s References: 592s >0 592s AGCATCGATCAGTATCTGA 592s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 592s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz 592s @HD VN:1.5 SO:unsorted GO:query 592s @SQ SN:0 LN:19 592s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz" 592s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 592s Fastq 2 (fw:1, sam:1) 592s References: 592s >0 592s AGCATCGATCAGTATCTGA 592s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz 592s @HD VN:1.5 SO:unsorted GO:query 592s @SQ SN:0 LN:19 592s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" 592s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 592s Fastq 3 (fw:1, sam:1) 592s References: 592s >0 592s AGCATCGATCAGTATCTGA 592s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz 593s @HD VN:1.5 SO:unsorted GO:query 593s @SQ SN:0 LN:19 593s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz" 593s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 593s Fastq 4 (fw:1, sam:1) 593s References: 593s >0 593s AGCATCGATCAGTATCTGA 593s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz 593s Error: Read r0 has more read characters than quality values. 593s terminate called after throwing an instance of 'int' 593s Aborted (core dumped) 593s (ERR): bowtie2-align exited with value 134 593s Fastq 5 (fw:1, sam:1) 593s References: 593s >0 593s AGCATCGATCAGTATCTGA 593s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz 593s Error: Read r0 has more read characters than quality values. 593s terminate called after throwing an instance of 'int' 593s Aborted (core dumped) 593s (ERR): bowtie2-align exited with value 134 593s Fastq 6 (fw:1, sam:1) 593s References: 593s >0 593s AGCATCGATCAGTATCTGA 593s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz 593s Error: reads file does not look like a FASTQ file 593s terminate called after throwing an instance of 'int' 594s Aborted (core dumped) 594s (ERR): bowtie2-align exited with value 134 594s Fastq 7 (fw:1, sam:1) 594s References: 594s >0 594s AGCATCGATCAGTATCTGA 594s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz 594s @HD VN:1.5 SO:unsorted GO:query 594s @SQ SN:0 LN:19 594s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz" 594s r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 594s Fastq 8 (fw:1, sam:1) 594s References: 594s >0 594s AGCATCGATCAGTATCTGA 594s /usr/bin/bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz 594s @HD VN:1.5 SO:unsorted GO:query 594s @SQ SN:0 LN:19 594s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz" 594s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 594s Fastq 9 (fw:1, sam:1) 594s References: 594s >0 594s AGCATCGATCAGTATCTGA 594s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz 594s @HD VN:1.5 SO:unsorted GO:query 594s @SQ SN:0 LN:19 594s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz" 594s Fastq multiread 1 (fw:1, sam:1) 594s References: 594s >0 594s AGCATCGATCAGTATCTGA 594s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz 594s @HD VN:1.5 SO:unsorted GO:query 594s @SQ SN:0 LN:19 594s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz" 594s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 594s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 594s Fastq multiread 2 (fw:1, sam:1) 594s References: 594s >0 594s AGCATCGATCAGTATCTGA 594s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz 594s @HD VN:1.5 SO:unsorted GO:query 594s @SQ SN:0 LN:19 594s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz" 594s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 594s Fastq multiread 3 (fw:1, sam:1) 594s References: 594s >0 594s AGCATCGATCAGTATCTGA 594s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz 594s @HD VN:1.5 SO:unsorted GO:query 594s @SQ SN:0 LN:19 594s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" 594s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 594s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 594s Fastq paired 1 (fw:1, sam:1) 594s References: 594s >0 594s AGCATCGATCAAAAACTGA 594s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 595s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 595s @HD VN:1.5 SO:unsorted GO:query 595s @SQ SN:0 LN:19 595s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 595s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 595s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 595s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 595s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 595s Fastq paired 2 (fw:1, sam:1) 595s References: 595s >0 595s AGCATCGATCAAAAACTGA 595s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 595s @HD VN:1.5 SO:unsorted GO:query 595s @SQ SN:0 LN:19 595s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 595s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 595s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 595s Fastq paired 3 (fw:1, sam:1) 595s References: 595s >0 595s AGCATCGATCAAAAACTGA 595s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 595s @HD VN:1.5 SO:unsorted GO:query 595s @SQ SN:0 LN:19 595s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 595s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 595s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 595s Fastq paired 4 (fw:1, sam:1) 595s References: 595s >0 595s AGCATCGATCAAAAACTGA 595s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 595s @HD VN:1.5 SO:unsorted GO:query 595s @SQ SN:0 LN:19 595s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 595s r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 595s r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 595s Fasta 1 (fw:1, sam:1) 595s References: 595s >0 595s AGCATCGATCAGTATCTGA 595s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 596s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz 596s @HD VN:1.5 SO:unsorted GO:query 596s @SQ SN:0 LN:19 596s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz" 596s r0 0 0 3 255 15M * 0 0 CATCGATCAGTATCT IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 596s Fasta 2 (fw:1, sam:1) 596s References: 596s >0 596s AGCATCGATCAGTATCTGA 596s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz 596s @HD VN:1.5 SO:unsorted GO:query 596s @SQ SN:0 LN:19 596s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" 596s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 596s Fasta 3 (fw:1, sam:1) 596s References: 596s >0 596s AGCATCGATCAGTATCTGA 596s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz 596s @HD VN:1.5 SO:unsorted GO:query 596s @SQ SN:0 LN:19 596s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz" 596s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 596s Fasta 5 (fw:1, sam:1) 596s References: 596s >0 596s AGCATCGATCAGTATCTGA 596s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz 596s Error: reads file does not look like a FASTA file 596s terminate called after throwing an instance of 'int' 597s Aborted (core dumped) 597s (ERR): bowtie2-align exited with value 134 597s Fasta 6 (fw:1, sam:1) 597s References: 597s >0 597s AGCATCGATCAGTATCTGA 597s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz 597s Error: reads file does not look like a FASTA file 597s terminate called after throwing an instance of 'int' 597s Aborted (core dumped) 597s (ERR): bowtie2-align exited with value 134 597s Fasta 7 (fw:1, sam:1) 597s References: 597s >0 597s AGCATCGATCAGTATCTGA 597s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz 597s @HD VN:1.5 SO:unsorted GO:query 597s @SQ SN:0 LN:19 597s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" 597s r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 597s Fasta 8 (fw:1, sam:1) 597s References: 597s >0 597s AGCATCGATCAGTATCTGA 597s /usr/bin/bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz 597s @HD VN:1.5 SO:unsorted GO:query 597s @SQ SN:0 LN:19 597s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz" 597s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 597s Fasta 9 (fw:1, sam:1) 597s References: 597s >0 597s AGCATCGATCAGTATCTGA 597s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz 597s @HD VN:1.5 SO:unsorted GO:query 597s @SQ SN:0 LN:19 597s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" 597s Fasta multiread 1 (fw:1, sam:1) 597s References: 597s >0 597s AGCATCGATCAGTATCTGA 597s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz 597s @HD VN:1.5 SO:unsorted GO:query 597s @SQ SN:0 LN:19 597s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz" 597s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 597s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 597s Fasta multiread 2 (fw:1, sam:1) 597s References: 597s >0 597s AGCATCGATCAGTATCTGA 597s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz 597s @HD VN:1.5 SO:unsorted GO:query 597s @SQ SN:0 LN:19 597s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz" 597s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 597s Fasta multiread 3 (fw:1, sam:1) 597s References: 597s >0 597s AGCATCGATCAGTATCTGA 597s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz 597s @HD VN:1.5 SO:unsorted GO:query 597s @SQ SN:0 LN:19 597s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" 597s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 597s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 597s Fasta multiline 1 (fw:1, sam:1) 597s References: 597s >0 597s AGCATCGATCAGTATCTGA 597s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz 598s @HD VN:1.5 SO:unsorted GO:query 598s @SQ SN:0 LN:19 598s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz" 598s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 598s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 598s Fasta multiline 2 (fw:1, sam:1) 598s References: 598s >0 598s AGCATCGATCAGTATCTGA 598s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz 598s @HD VN:1.5 SO:unsorted GO:query 598s @SQ SN:0 LN:19 598s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz" 598s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 598s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 598s Fasta multiline 3 (fw:1, sam:1) 598s References: 598s >0 598s AGCATCGATCAGTATCTGA 598s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz 598s @HD VN:1.5 SO:unsorted GO:query 598s @SQ SN:0 LN:19 598s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz" 598s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 598s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 598s Fasta paired 1 (fw:1, sam:1) 598s References: 598s >0 598s AGCATCGATCAAAAACTGA 598s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 598s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 598s @HD VN:1.5 SO:unsorted GO:query 598s @SQ SN:0 LN:19 598s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 598s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 598s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 598s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 598s r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP 598s Fasta paired 2 (fw:1, sam:1) 598s References: 598s >0 598s AGCATCGATCAAAAACTGA 598s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 598s @HD VN:1.5 SO:unsorted GO:query 598s @SQ SN:0 LN:19 598s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 598s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 598s r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP 598s Fasta paired 3 (fw:1, sam:1) 598s References: 598s >0 598s AGCATCGATCAAAAACTGA 598s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 598s @HD VN:1.5 SO:unsorted GO:query 598s @SQ SN:0 LN:19 598s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 598s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 598s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 598s Fasta paired 4 (fw:1, sam:1) 598s References: 598s >0 598s AGCATCGATCAAAAACTGA 598s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 598s @HD VN:1.5 SO:unsorted GO:query 598s @SQ SN:0 LN:19 598s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 598s 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 598s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 598s Raw 1 (fw:1, sam:1) 598s References: 598s >0 598s AGCATCGATCAGTATCTGA 598s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 598s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz 598s @HD VN:1.5 SO:unsorted GO:query 598s @SQ SN:0 LN:19 598s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz" 598s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 598s Raw 2 (fw:1, sam:1) 598s References: 598s >0 598s AGCATCGATCAGTATCTGA 598s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz 599s @HD VN:1.5 SO:unsorted GO:query 599s @SQ SN:0 LN:19 599s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz" 599s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 599s Raw 3 (fw:1, sam:1) 599s References: 599s >0 599s AGCATCGATCAGTATCTGA 599s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz 599s @HD VN:1.5 SO:unsorted GO:query 599s @SQ SN:0 LN:19 599s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz" 599s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 599s Raw 7 (fw:1, sam:1) 599s References: 599s >0 599s AGCATCGATCAGTATCTGA 599s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz 599s @HD VN:1.5 SO:unsorted GO:query 599s @SQ SN:0 LN:19 599s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz" 599s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 599s Raw 8 (fw:1, sam:1) 599s References: 599s >0 599s AGCATCGATCAGTATCTGA 599s /usr/bin/bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz 599s @HD VN:1.5 SO:unsorted GO:query 599s @SQ SN:0 LN:19 599s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz" 599s 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 599s Raw 9 (fw:1, sam:1) 599s References: 599s >0 599s AGCATCGATCAGTATCTGA 599s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz 599s @HD VN:1.5 SO:unsorted GO:query 599s @SQ SN:0 LN:19 599s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz" 599s Raw multiread 1 (fw:1, sam:1) 599s References: 599s >0 599s AGCATCGATCAGTATCTGA 599s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz 599s @HD VN:1.5 SO:unsorted GO:query 599s @SQ SN:0 LN:19 599s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz" 599s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 599s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 599s Raw multiread 2 (fw:1, sam:1) 599s References: 599s >0 599s AGCATCGATCAGTATCTGA 599s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz 599s @HD VN:1.5 SO:unsorted GO:query 599s @SQ SN:0 LN:19 599s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz" 599s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 599s Raw multiread 3 (fw:1, sam:1) 599s References: 599s >0 599s AGCATCGATCAGTATCTGA 599s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r .simple_tests.raw.gz 599s @HD VN:1.5 SO:unsorted GO:query 599s @SQ SN:0 LN:19 599s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r .simple_tests.raw.gz" 599s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 599s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 599s Raw paired 1 (fw:1, sam:1) 599s References: 599s >0 599s AGCATCGATCAAAAACTGA 599s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 600s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 600s @HD VN:1.5 SO:unsorted GO:query 600s @SQ SN:0 LN:19 600s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 600s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 600s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 600s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 600s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 600s Raw paired 2 (fw:1, sam:1) 600s References: 600s >0 600s AGCATCGATCAAAAACTGA 600s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 600s @HD VN:1.5 SO:unsorted GO:query 600s @SQ SN:0 LN:19 600s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 600s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 600s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 600s Raw paired 3 (fw:1, sam:1) 600s References: 600s >0 600s AGCATCGATCAAAAACTGA 600s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 600s @HD VN:1.5 SO:unsorted GO:query 600s @SQ SN:0 LN:19 600s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 600s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 600s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 600s Raw paired 4 (fw:1, sam:1) 600s References: 600s >0 600s AGCATCGATCAAAAACTGA 600s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 600s @HD VN:1.5 SO:unsorted GO:query 600s @SQ SN:0 LN:19 600s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 600s 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 600s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 600s Tabbed 1 (fw:1, sam:1) 600s References: 600s >0 600s AGCATCGATCAGTATCTGA 600s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 600s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 601s @HD VN:1.5 SO:unsorted GO:query 601s @SQ SN:0 LN:19 601s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 601s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 601s Tabbed 2 (fw:1, sam:1) 601s References: 601s >0 601s AGCATCGATCAGTATCTGA 601s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 601s @HD VN:1.5 SO:unsorted GO:query 601s @SQ SN:0 LN:19 601s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 601s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 601s Tabbed 3 (fw:1, sam:1) 601s References: 601s >0 601s AGCATCGATCAGTATCTGA 601s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 601s @HD VN:1.5 SO:unsorted GO:query 601s @SQ SN:0 LN:19 601s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 601s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 601s Tabbed 4 (fw:1, sam:1) 601s References: 601s >0 601s AGCATCGATCAGTATCTGA 601s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 601s Error: Read r0 has more read characters than quality values. 601s terminate called after throwing an instance of 'int' 601s Aborted (core dumped) 601s (ERR): bowtie2-align exited with value 134 601s Tabbed 5 (fw:1, sam:1) 601s References: 601s >0 601s AGCATCGATCAGTATCTGA 601s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 601s Error: Read r0 has more quality values than read characters. 601s terminate called after throwing an instance of 'int' 602s Aborted (core dumped) 602s (ERR): bowtie2-align exited with value 134 602s Tabbed 7 (fw:1, sam:1) 602s References: 602s >0 602s AGCATCGATCAGTATCTGA 602s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 602s @HD VN:1.5 SO:unsorted GO:query 602s @SQ SN:0 LN:19 602s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 602s r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 602s Tabbed 8 (fw:1, sam:1) 602s References: 602s >0 602s AGCATCGATCAGTATCTGA 602s /usr/bin/bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 602s @HD VN:1.5 SO:unsorted GO:query 602s @SQ SN:0 LN:19 602s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 602s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 602s Tabbed 9 (fw:1, sam:1) 602s References: 602s >0 602s AGCATCGATCAGTATCTGA 602s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 602s @HD VN:1.5 SO:unsorted GO:query 602s @SQ SN:0 LN:19 602s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 602s Tabbed multiread 1 (fw:1, sam:1) 602s References: 602s >0 602s AGCATCGATCAGTATCTGA 602s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 602s @HD VN:1.5 SO:unsorted GO:query 602s @SQ SN:0 LN:19 602s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 602s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 602s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 602s Tabbed multiread 2 (fw:1, sam:1) 602s References: 602s >0 602s AGCATCGATCAGTATCTGA 602s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 602s @HD VN:1.5 SO:unsorted GO:query 602s @SQ SN:0 LN:19 602s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 602s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 602s Tabbed multiread 3 (fw:1, sam:1) 602s References: 602s >0 602s AGCATCGATCAGTATCTGA 602s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 602s @HD VN:1.5 SO:unsorted GO:query 602s @SQ SN:0 LN:19 602s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 602s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 602s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 602s Tabbed paired 1 (fw:1, sam:1) 602s References: 602s >0 602s AGCATCGATCAAAAACTGA 602s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 603s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 603s @HD VN:1.5 SO:unsorted GO:query 603s @SQ SN:0 LN:19 603s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 603s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 603s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 603s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 603s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 603s Tabbed paired 2 (fw:1, sam:1) 603s References: 603s >0 603s AGCATCGATCAAAAACTGA 603s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 603s @HD VN:1.5 SO:unsorted GO:query 603s @SQ SN:0 LN:19 603s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 603s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 603s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 603s Tabbed paired 3 (fw:1, sam:1) 603s References: 603s >0 603s AGCATCGATCAAAAACTGA 603s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 603s @HD VN:1.5 SO:unsorted GO:query 603s @SQ SN:0 LN:19 603s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 603s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 603s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 603s Tabbed paired 4 (fw:1, sam:1) 603s References: 603s >0 603s AGCATCGATCAAAAACTGA 603s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:19 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 606s r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 606s r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 606s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 606s Qseq 1 (fw:1, sam:1) 606s References: 606s >0 606s AGCATCGATCAGTATCTGA 606s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 606s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:19 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 606s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 606s Qseq 2 (fw:1, sam:1) 606s References: 606s >0 606s AGCATCGATCAGTATCTGA 606s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:19 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 606s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 606s Qseq 3 (fw:1, sam:1) 606s References: 606s >0 606s AGCATCGATCAGTATCTGA 606s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:19 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 606s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 606s Qseq 4 (fw:1, sam:1) 606s References: 606s >0 606s AGCATCGATCAGTATCTGA 606s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 606s Qseq 7 (fw:1, sam:1) 606s References: 606s >0 606s AGCATCGATCAGTATCTGA 606s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:19 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 606s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 606s Qseq 8 (fw:1, sam:1) 606s References: 606s >0 606s AGCATCGATCAGTATCTGA 606s /usr/bin/bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:19 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 606s MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 606s Qseq 9 (fw:1, sam:1) 606s References: 606s >0 606s AGCATCGATCAGTATCTGA 606s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:19 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 606s Qseq multiread 1 (fw:1, sam:1) 606s References: 606s >0 606s AGCATCGATCAGTATCTGA 606s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:19 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 606s MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 606s MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 606s Qseq multiread 2 (fw:1, sam:1) 606s References: 606s >0 606s AGCATCGATCAGTATCTGA 606s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:19 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 606s MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 606s Qseq multiread 3 (fw:1, sam:1) 606s References: 606s >0 606s AGCATCGATCAGTATCTGA 606s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:19 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 606s MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 606s MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 606s Qseq paired 1 (fw:1, sam:1) 606s References: 606s >0 606s AGCATCGATCAAAAACTGA 606s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 606s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:19 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" 606s MachName_RunNum_Lane_Tile_10_10_Index 99 0 1 255 10M = 9 19 AGCATCGATC ABCBGACBCB AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 606s MachName_RunNum_Lane_Tile_10_10_Index 147 0 9 255 11M = 1 -19 TCAAAAACTGA ABCBCAGBCBA AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 606s MachName_RunNum_Lane_Tile_12_15_Index 83 0 9 255 11M = 1 -19 TCAAAAACTGA 57865494859 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 606s MachName_RunNum_Lane_Tile_12_15_Index 163 0 1 255 10M = 9 19 AGCATCGATC AGGCBBGCBG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 606s Qseq paired 2 (fw:1, sam:1) 606s References: 606s >0 606s AGCATCGATCAAAAACTGA 606s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:19 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" 606s MachName_RunNum_Lane_Tile_12_15_Index 83 0 9 255 11M = 1 -19 TCAAAAACTGA 57865494859 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 606s MachName_RunNum_Lane_Tile_12_15_Index 163 0 1 255 10M = 9 19 AGCATCGATC AGGCBBGCBG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 606s Left-align insertion (fw:1, sam:1) 606s References: 606s >0 606s GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 606s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 606s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 606s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 606s Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values. 606s terminate called after throwing an instance of 'int' 606s Aborted (core dumped) 606s (ERR): bowtie2-align exited with value 134 606s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 606s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 606s /usr/bin/bowtie2 --large-index --quiet --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:73 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 606s r0 0 0 23 24 2M1I40M * 0 0 ACAAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:42 YT:Z:UU 606s Left-align deletion (fw:1, sam:1) 606s References: 606s >0 606s GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 606s /usr/bin/bowtie2 --large-index --quiet --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 606s @HD VN:1.5 SO:unsorted GO:query 606s @SQ SN:0 LN:73 606s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 606s r0 0 0 19 40 6M1D39M * 0 0 ACGTACAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^A39 YT:Z:UU 606s Left-align insertion with mismatch at LHS (fw:1, sam:1) 606s References: 606s >0 606s GCGATATCTACGACTGCTACGCCCAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 606s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 607s /usr/bin/bowtie2 --large-index --quiet --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 607s @HD VN:1.5 SO:unsorted GO:query 607s @SQ SN:0 LN:73 607s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 607s r0 0 0 5 24 20M1D45M * 0 0 TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:20^A0A44 YT:Z:UU 607s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 607s References: 607s >0 607s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG 607s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 607s /usr/bin/bowtie2 --large-index --fr --quiet --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 607s @HD VN:1.5 SO:unsorted GO:query 607s @SQ SN:0 LN:1192 607s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 607s r0 65 0 3 42 38M = 1065 0 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UP 607s r0 129 0 1065 1 42M = 3 0 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YT:Z:UP 607s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 607s References: 607s >0 607s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG 607s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 607s /usr/bin/bowtie2 --large-index --fr --quiet --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 607s @HD VN:1.5 SO:unsorted GO:query 607s @SQ SN:0 LN:1028 607s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 607s r0 65 0 3 42 38M = 982 1021 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:DP 607s r0 129 0 982 42 42M = 3 -1021 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:DP 607s MREVERSE flag is set if mate does not align (fw:1, sam:1) 607s References: 607s >0 607s TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG 607s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 608s /usr/bin/bowtie2 --large-index --fr --quiet --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 608s @HD VN:1.5 SO:unsorted GO:query 608s @SQ SN:0 LN:250 608s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 608s r0 89 0 51 42 100M = 51 0 TTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UP 608s r0 165 0 51 0 * = 51 0 CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 608s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 608s References: 608s >0 608s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG 608s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 608s /usr/bin/bowtie2 --large-index --fr --quiet --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 608s @HD VN:1.5 SO:unsorted GO:query 608s @SQ SN:0 LN:290 608s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 608s r0 99 0 3 1 38M = 246 285 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:CP 608s r0 147 0 246 1 42M = 3 -285 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:CP 608s MD:Z 1 (fw:1, sam:1) 608s References: 608s >0 608s CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 608s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 608s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 608s @HD VN:1.5 SO:unsorted GO:query 608s @SQ SN:0 LN:54 608s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 608s r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU 608s MD:Z 1 (fw:0, sam:1) 608s References: 608s >0 608s CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 608s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 609s @HD VN:1.5 SO:unsorted GO:query 609s @SQ SN:0 LN:54 609s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 609s r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU 609s MD:Z 2 (fw:1, sam:1) 609s References: 609s >0 609s CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 609s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 609s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 609s @HD VN:1.5 SO:unsorted GO:query 609s @SQ SN:0 LN:54 609s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 609s r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU 609s MD:Z 2 (fw:0, sam:1) 609s References: 609s >0 609s CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 609s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 609s @HD VN:1.5 SO:unsorted GO:query 609s @SQ SN:0 LN:54 609s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 609s r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU 609s MD:Z 3 (fw:1, sam:1) 609s References: 609s >0 609s CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 609s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 610s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 610s @HD VN:1.5 SO:unsorted GO:query 610s @SQ SN:0 LN:55 610s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 610s r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU 610s MD:Z 3 (fw:0, sam:1) 610s References: 610s >0 610s CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 610s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 610s @HD VN:1.5 SO:unsorted GO:query 610s @SQ SN:0 LN:55 610s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 610s r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU 610s MD:Z 4 (fw:1, sam:1) 610s References: 610s >0 610s CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 610s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 610s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 610s @HD VN:1.5 SO:unsorted GO:query 610s @SQ SN:0 LN:55 610s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 610s r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:3 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^NN0N39 YT:Z:UU 610s MD:Z 4 (fw:0, sam:1) 610s References: 610s >0 610s CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 610s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 610s @HD VN:1.5 SO:unsorted GO:query 610s @SQ SN:0 LN:55 610s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 610s r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:3 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^NN0N39 YT:Z:UU 610s Local alignment 1 (fw:1, sam:1) 610s References: 610s >0 610s TTGT 610s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 611s /usr/bin/bowtie2 --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 611s @HD VN:1.5 SO:unsorted GO:query 611s @SQ SN:0 LN:4 611s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 611s r0 0 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU 611s Local alignment 1 (fw:0, sam:1) 611s References: 611s >0 611s TTGT 611s /usr/bin/bowtie2 --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 611s @HD VN:1.5 SO:unsorted GO:query 611s @SQ SN:0 LN:4 611s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 611s r0 16 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU 611s Local alignment 2 (fw:1, sam:1) 611s References: 611s >0 611s TTGA 611s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 611s /usr/bin/bowtie2 --large-index --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 611s @HD VN:1.5 SO:unsorted GO:query 611s @SQ SN:0 LN:4 611s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 611s r0 0 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 611s Local alignment 2 (fw:0, sam:1) 611s References: 611s >0 611s TTGA 611s /usr/bin/bowtie2 --large-index --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 611s @HD VN:1.5 SO:unsorted GO:query 611s @SQ SN:0 LN:4 611s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 611s r0 16 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 611s Local alignment 3 (fw:1, sam:1) 611s References: 611s >0 611s TTGTTCGTTTGTTCGT 611s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 611s /usr/bin/bowtie2 --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 612s @HD VN:1.5 SO:unsorted GO:query 612s @SQ SN:0 LN:16 612s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 612s r0 0 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 612s r0 256 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 612s Local alignment 3 (fw:0, sam:1) 612s References: 612s >0 612s TTGTTCGTTTGTTCGT 612s /usr/bin/bowtie2 --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 612s @HD VN:1.5 SO:unsorted GO:query 612s @SQ SN:0 LN:16 612s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 612s r0 16 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 612s r0 272 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 612s Local alignment 4 (fw:1, sam:1) 612s References: 612s >0 612s TTGTTCGTTTGTTCGT 612s /usr/bin/bowtie2 --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 612s @HD VN:1.5 SO:unsorted GO:query 612s @SQ SN:0 LN:16 612s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 612s r0 0 0 1 37 12M * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:24 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 612s r0 256 0 9 255 8M4S * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 612s Local alignment 4 (fw:0, sam:1) 612s References: 612s >0 612s TTGTTCGTTTGTTCGT 612s /usr/bin/bowtie2 --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 612s @HD VN:1.5 SO:unsorted GO:query 612s @SQ SN:0 LN:16 612s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 612s r0 16 0 1 37 12M * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:24 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 612s r0 272 0 9 255 8M4S * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 612s Alignment order -k (fw:1, sam:1) 612s References: 612s >0 612s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 612s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 612s /usr/bin/bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 612s @HD VN:1.5 SO:unsorted GO:query 612s @SQ SN:0 LN:86 612s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 612s r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 612s r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 612s r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 612s r0 256 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 612s Alignment order -k (fw:0, sam:1) 612s References: 612s >0 612s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 612s /usr/bin/bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 613s @HD VN:1.5 SO:unsorted GO:query 613s @SQ SN:0 LN:86 613s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 613s r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 613s r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 613s r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 613s r0 272 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 613s Alignment order -a (fw:1, sam:1) 613s References: 613s >0 613s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 613s /usr/bin/bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 613s @HD VN:1.5 SO:unsorted GO:query 613s @SQ SN:0 LN:86 613s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 613s r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 613s r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 613s r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 613s r0 256 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 613s Alignment order -a (fw:0, sam:1) 613s References: 613s >0 613s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 613s /usr/bin/bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 613s @HD VN:1.5 SO:unsorted GO:query 613s @SQ SN:0 LN:86 613s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 613s r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 613s r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 613s r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 613s r0 272 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 613s Mate reporting order, -a (fw:1, sam:1) 613s References: 613s >0 613s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 613s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 613s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 614s @HD VN:1.5 SO:unsorted GO:query 614s @SQ SN:0 LN:407 614s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 614s r0 99 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 147 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 355 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 403 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 355 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 403 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 403 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 355 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 403 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 355 0 3 255 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 403 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 339 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 419 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 339 0 169 255 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 419 0 104 255 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 339 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 419 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 419 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 339 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 419 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r2 99 0 307 255 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 614s r2 147 0 379 255 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 614s Mate reporting order, -a (fw:0, sam:1) 614s References: 614s >0 614s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 614s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 614s @HD VN:1.5 SO:unsorted GO:query 614s @SQ SN:0 LN:407 614s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 614s r0 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 339 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 419 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 339 0 169 255 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 419 0 104 255 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 339 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 419 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 419 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 339 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 419 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 99 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 147 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 355 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 403 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 355 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 403 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 403 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 355 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 403 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 355 0 3 255 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 403 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r2 83 0 379 255 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 614s r2 163 0 307 255 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 614s Mate reporting order, -M 1 (fw:1, sam:1) 614s References: 614s >0 614s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 614s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 614s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 614s @HD VN:1.5 SO:unsorted GO:query 614s @SQ SN:0 LN:407 614s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 614s r0 99 0 104 1 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 147 0 270 1 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 83 0 270 1 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 163 0 104 1 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r2 99 0 307 42 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 614s r2 147 0 379 42 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 614s Mate reporting order, -M 1 (fw:0, sam:1) 614s References: 614s >0 614s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 614s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 614s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 614s @HD VN:1.5 SO:unsorted GO:query 614s @SQ SN:0 LN:407 614s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 614s r0 83 0 270 1 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r0 163 0 104 1 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 99 0 104 1 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r1 147 0 270 1 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 614s r2 83 0 379 42 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 614s r2 163 0 307 42 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 614s Non-overlapping; no args (fw:1, sam:1) 614s References: 614s >0 614s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 614s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 614s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 615s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 615s @HD VN:1.5 SO:unsorted GO:query 615s @SQ SN:0 LN:47 615s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 615s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 615s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 615s Non-overlapping; no args (fw:0, sam:1) 615s References: 615s >0 615s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 615s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 615s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 615s @HD VN:1.5 SO:unsorted GO:query 615s @SQ SN:0 LN:47 615s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 615s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 615s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 615s Non-overlapping; --no-discordant (fw:1, sam:1) 615s References: 615s >0 615s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 615s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 615s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 615s @HD VN:1.5 SO:unsorted GO:query 615s @SQ SN:0 LN:47 615s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 615s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 615s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 615s Non-overlapping; --no-discordant (fw:0, sam:1) 615s References: 615s >0 615s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 615s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 615s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 615s @HD VN:1.5 SO:unsorted GO:query 615s @SQ SN:0 LN:47 615s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 615s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 615s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 615s Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) 615s References: 615s >0 615s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 615s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 615s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 615s @HD VN:1.5 SO:unsorted GO:query 615s @SQ SN:0 LN:47 615s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 615s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 615s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 615s Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) 615s References: 615s >0 615s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 615s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 615s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 615s @HD VN:1.5 SO:unsorted GO:query 615s @SQ SN:0 LN:47 615s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 615s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 615s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 615s Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) 615s References: 615s >0 615s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 615s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 615s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 615s @HD VN:1.5 SO:unsorted GO:query 615s @SQ SN:0 LN:47 615s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 615s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 615s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 615s Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) 615s References: 615s >0 615s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 615s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 616s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 616s @HD VN:1.5 SO:unsorted GO:query 616s @SQ SN:0 LN:47 616s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 616s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 616s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 616s Non-overlapping; --no-dovetail (fw:1, sam:1) 616s References: 616s >0 616s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 616s /usr/bin/bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 616s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 616s @HD VN:1.5 SO:unsorted GO:query 616s @SQ SN:0 LN:47 616s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 616s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 616s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 616s Non-overlapping; --no-dovetail (fw:0, sam:1) 616s References: 616s >0 616s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 616s /usr/bin/bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 616s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 616s @HD VN:1.5 SO:unsorted GO:query 616s @SQ SN:0 LN:47 616s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 616s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 616s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 616s Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1) 616s References: 616s >0 616s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 616s /usr/bin/bowtie2 --large-index --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 616s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 616s @HD VN:1.5 SO:unsorted GO:query 616s @SQ SN:0 LN:47 616s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 616s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 616s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 616s Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1) 616s References: 616s >0 616s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 616s /usr/bin/bowtie2 --large-index --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 616s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 616s @HD VN:1.5 SO:unsorted GO:query 616s @SQ SN:0 LN:47 616s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 616s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 616s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 616s Non-overlapping; --no-overlap (fw:1, sam:1) 616s References: 616s >0 616s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 616s /usr/bin/bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 616s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 616s @HD VN:1.5 SO:unsorted GO:query 616s @SQ SN:0 LN:47 616s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 616s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 616s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 616s Non-overlapping; --no-overlap (fw:0, sam:1) 616s References: 616s >0 616s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 616s /usr/bin/bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 616s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 617s @HD VN:1.5 SO:unsorted GO:query 617s @SQ SN:0 LN:47 617s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 617s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 617s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 617s Overlapping; no args (fw:1, sam:1) 617s References: 617s >0 617s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 617s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 617s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 617s @HD VN:1.5 SO:unsorted GO:query 617s @SQ SN:0 LN:47 617s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 617s r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 617s r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 617s Overlapping; no args (fw:0, sam:1) 617s References: 617s >0 617s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 617s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 617s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 617s @HD VN:1.5 SO:unsorted GO:query 617s @SQ SN:0 LN:47 617s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 617s r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 617s r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 617s Overlapping; --no-dovetail (fw:1, sam:1) 617s References: 617s >0 617s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 617s /usr/bin/bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 617s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 617s @HD VN:1.5 SO:unsorted GO:query 617s @SQ SN:0 LN:47 617s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 617s r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 617s r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 617s Overlapping; --no-dovetail (fw:0, sam:1) 617s References: 617s >0 617s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 617s /usr/bin/bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 617s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 617s @HD VN:1.5 SO:unsorted GO:query 617s @SQ SN:0 LN:47 617s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 617s r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 617s r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 617s Overlapping; --no-contain (fw:1, sam:1) 617s References: 617s >0 617s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 617s /usr/bin/bowtie2 --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 617s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 617s @HD VN:1.5 SO:unsorted GO:query 617s @SQ SN:0 LN:47 617s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 617s r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 617s r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 617s Overlapping; --no-contain (fw:0, sam:1) 617s References: 617s >0 617s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 617s /usr/bin/bowtie2 --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 617s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 617s @HD VN:1.5 SO:unsorted GO:query 617s @SQ SN:0 LN:47 617s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 617s r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 617s r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 617s Overlapping; --no-overlap (fw:1, sam:1) 617s References: 617s >0 617s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 617s /usr/bin/bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 617s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 617s @HD VN:1.5 SO:unsorted GO:query 617s @SQ SN:0 LN:47 617s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 617s r0 65 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP 617s r0 129 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:DP 617s Overlapping; --no-overlap (fw:0, sam:1) 617s References: 617s >0 617s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 617s /usr/bin/bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 617s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 617s @HD VN:1.5 SO:unsorted GO:query 617s @SQ SN:0 LN:47 617s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 617s r0 113 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:DP 617s r0 177 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP 617s Scoring params 1 (fw:1, sam:1) 617s References: 617s >0 617s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG 617s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 618s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 618s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 618s @HD VN:1.5 SO:unsorted GO:query 618s @SQ SN:0 LN:105 618s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 618s r0 0 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU 618s Scoring params 1 (fw:0, sam:1) 618s References: 618s >0 618s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG 618s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 618s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 618s @HD VN:1.5 SO:unsorted GO:query 618s @SQ SN:0 LN:105 618s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 618s r0 16 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU 618s Scoring params 2 (fw:1, sam:1) 618s References: 618s >0 618s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 618s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 618s /usr/bin/bowtie2 --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 618s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 619s @HD VN:1.5 SO:unsorted GO:query 619s @SQ SN:0 LN:102 619s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 619s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 619s Scoring params 2 (fw:0, sam:1) 619s References: 619s >0 619s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 619s /usr/bin/bowtie2 --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 619s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 619s @HD VN:1.5 SO:unsorted GO:query 619s @SQ SN:0 LN:102 619s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 619s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 619s Scoring params 3 (fw:1, sam:1) 619s References: 619s >0 619s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 619s /usr/bin/bowtie2 --large-index --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 619s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 619s @HD VN:1.5 SO:unsorted GO:query 619s @SQ SN:0 LN:102 619s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 619s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 619s Scoring params 3 (fw:0, sam:1) 619s References: 619s >0 619s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 619s /usr/bin/bowtie2 --large-index --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 619s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 619s @HD VN:1.5 SO:unsorted GO:query 619s @SQ SN:0 LN:102 619s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 619s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 619s Scoring params 4 (fw:1, sam:1) 619s References: 619s >0 619s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 619s /usr/bin/bowtie2 --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 619s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 619s @HD VN:1.5 SO:unsorted GO:query 619s @SQ SN:0 LN:102 619s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 619s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 619s Scoring params 4 (fw:0, sam:1) 619s References: 619s >0 619s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 619s /usr/bin/bowtie2 --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 619s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 619s @HD VN:1.5 SO:unsorted GO:query 619s @SQ SN:0 LN:102 619s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 619s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 619s Scoring params 5 (fw:1, sam:1) 619s References: 619s >0 619s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 619s /usr/bin/bowtie2 --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 619s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 619s @HD VN:1.5 SO:unsorted GO:query 619s @SQ SN:0 LN:102 619s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 619s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-40 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 619s Scoring params 5 (fw:0, sam:1) 619s References: 619s >0 619s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 619s /usr/bin/bowtie2 --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 619s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 619s @HD VN:1.5 SO:unsorted GO:query 619s @SQ SN:0 LN:102 619s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 619s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-40 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 619s Scoring params 6 (fw:1, sam:1) 619s References: 619s >0 619s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 619s /usr/bin/bowtie2 --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 620s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 620s @HD VN:1.5 SO:unsorted GO:query 620s @SQ SN:0 LN:102 620s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 620s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 620s Scoring params 6 (fw:0, sam:1) 620s References: 620s >0 620s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 620s /usr/bin/bowtie2 --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 620s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 620s @HD VN:1.5 SO:unsorted GO:query 620s @SQ SN:0 LN:102 620s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 620s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 620s Q XS:i 1a (fw:1, sam:1) 620s References: 620s >0 620s TTGTTCGATTGTTCGA 620s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 620s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 620s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 620s @HD VN:1.5 SO:unsorted GO:query 620s @SQ SN:0 LN:16 620s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 620s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 620s Q XS:i 1a (fw:0, sam:1) 620s References: 620s >0 620s TTGTTCGATTGTTCGA 620s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 620s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 620s @HD VN:1.5 SO:unsorted GO:query 620s @SQ SN:0 LN:16 620s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 620s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 620s Q XS:i 1a ! --mp 3,3 (fw:1, sam:1) 620s References: 620s >0 620s TTGTTCGATTGTTCGA 620s /usr/bin/bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 620s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 620s @HD VN:1.5 SO:unsorted GO:query 620s @SQ SN:0 LN:16 620s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 620s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 620s Q XS:i 1a ! --mp 3,3 (fw:0, sam:1) 620s References: 620s >0 620s TTGTTCGATTGTTCGA 620s /usr/bin/bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 621s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 621s @HD VN:1.5 SO:unsorted GO:query 621s @SQ SN:0 LN:16 621s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 621s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 621s Q XS:i 1a ! --mp 3,6 (fw:1, sam:1) 621s References: 621s >0 621s TTGTTCGATTGTTCGA 621s /usr/bin/bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 621s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 621s @HD VN:1.5 SO:unsorted GO:query 621s @SQ SN:0 LN:16 621s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 621s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 621s Q XS:i 1a ! --mp 3,6 (fw:0, sam:1) 621s References: 621s >0 621s TTGTTCGATTGTTCGA 621s /usr/bin/bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 621s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 621s @HD VN:1.5 SO:unsorted GO:query 621s @SQ SN:0 LN:16 621s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 621s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 621s Q XS:i 1a I --mp 3,3 (fw:1, sam:1) 621s References: 621s >0 621s TTGTTCGATTGTTCGA 621s /usr/bin/bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 621s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 621s @HD VN:1.5 SO:unsorted GO:query 621s @SQ SN:0 LN:16 621s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 621s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 621s Q XS:i 1a I --mp 3,3 (fw:0, sam:1) 621s References: 621s >0 621s TTGTTCGATTGTTCGA 621s /usr/bin/bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 621s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 621s @HD VN:1.5 SO:unsorted GO:query 621s @SQ SN:0 LN:16 621s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 621s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 621s Q XS:i 1a I --mp 3,6 (fw:1, sam:1) 621s References: 621s >0 621s TTGTTCGATTGTTCGA 621s /usr/bin/bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 621s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 621s @HD VN:1.5 SO:unsorted GO:query 621s @SQ SN:0 LN:16 621s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 621s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 621s Q XS:i 1a I --mp 3,6 (fw:0, sam:1) 621s References: 621s >0 621s TTGTTCGATTGTTCGA 621s /usr/bin/bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 621s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 621s @HD VN:1.5 SO:unsorted GO:query 621s @SQ SN:0 LN:16 621s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 621s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 621s Q XS:i 1a --ignore-quals (fw:1, sam:1) 621s References: 621s >0 621s TTGTTCGATTGTTCGA 621s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 621s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 621s @HD VN:1.5 SO:unsorted GO:query 621s @SQ SN:0 LN:16 621s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 621s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 621s Q XS:i 1a --ignore-quals (fw:0, sam:1) 621s References: 621s >0 621s TTGTTCGATTGTTCGA 621s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 621s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 621s @HD VN:1.5 SO:unsorted GO:query 621s @SQ SN:0 LN:16 621s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 621s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 621s Q XS:i 1b (fw:1, sam:1) 621s References: 621s >0 621s TTGTTCGATTGTTCGA 621s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 622s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 622s @HD VN:1.5 SO:unsorted GO:query 622s @SQ SN:0 LN:16 622s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 622s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-4 XS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 622s Q XS:i 1b (fw:0, sam:1) 622s References: 622s >0 622s TTGTTCGATTGTTCGA 622s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 622s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 622s @HD VN:1.5 SO:unsorted GO:query 622s @SQ SN:0 LN:16 622s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 622s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-4 XS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 622s Q XS:i 1b --ignore-quals (fw:1, sam:1) 622s References: 622s >0 622s TTGTTCGATTGTTCGA 622s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 622s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 622s @HD VN:1.5 SO:unsorted GO:query 622s @SQ SN:0 LN:16 622s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 622s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 622s Q XS:i 1b --ignore-quals (fw:0, sam:1) 622s References: 622s >0 622s TTGTTCGATTGTTCGA 622s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 622s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 622s @HD VN:1.5 SO:unsorted GO:query 622s @SQ SN:0 LN:16 622s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 622s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 622s Q XS:i 1c (fw:1, sam:1) 622s References: 622s >0 622s TTGTTCGATTGTTCGA 622s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 622s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 622s @HD VN:1.5 SO:unsorted GO:query 622s @SQ SN:0 LN:16 622s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 622s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 622s Q XS:i 1c (fw:0, sam:1) 622s References: 622s >0 622s TTGTTCGATTGTTCGA 622s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 622s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 622s @HD VN:1.5 SO:unsorted GO:query 622s @SQ SN:0 LN:16 622s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 622s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 622s Q XS:i 1c --ignore-quals (fw:1, sam:1) 622s References: 622s >0 622s TTGTTCGATTGTTCGA 622s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 622s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 622s @HD VN:1.5 SO:unsorted GO:query 622s @SQ SN:0 LN:16 622s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 622s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 622s Q XS:i 1c --ignore-quals (fw:0, sam:1) 622s References: 622s >0 622s TTGTTCGATTGTTCGA 622s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 623s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 623s @HD VN:1.5 SO:unsorted GO:query 623s @SQ SN:0 LN:16 623s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 623s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 623s (fw:1, sam:1) 623s References: 623s >0 623s CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT 623s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 623s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 623s @HD VN:1.5 SO:unsorted GO:query 623s @SQ SN:0 LN:68 623s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 623s r0 73 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP 623s r0 133 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 623s (fw:0, sam:1) 623s References: 623s >0 623s CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT 623s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 623s @HD VN:1.5 SO:unsorted GO:query 623s @SQ SN:0 LN:68 623s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 623s r0 137 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP 623s r0 69 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 623s (fw:1, sam:1) 623s References: 623s >0 623s TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT 623s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 623s /usr/bin/bowtie2 --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 623s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 623s @HD VN:1.5 SO:unsorted GO:query 623s @SQ SN:0 LN:528 623s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 623s r0 0 0 457 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 623s (fw:0, sam:1) 623s References: 623s >0 623s TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT 623s /usr/bin/bowtie2 --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 624s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 624s @HD VN:1.5 SO:unsorted GO:query 624s @SQ SN:0 LN:528 624s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 624s r0 16 0 289 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 624s (fw:1, sam:1) 624s References: 624s >0 624s TTGTTCGTTTGTTCGT 624s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 624s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 624s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 624s @HD VN:1.5 SO:unsorted GO:query 624s @SQ SN:0 LN:16 624s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 624s r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 624s (fw:0, sam:1) 624s References: 624s >0 624s TTGTTCGTTTGTTCGT 624s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 624s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 624s @HD VN:1.5 SO:unsorted GO:query 624s @SQ SN:0 LN:16 624s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 624s r0 16 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 624s (fw:1, sam:1) 624s References: 624s >0 624s TTGTTCGTTTGTTCGT 624s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 624s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 624s @HD VN:1.5 SO:unsorted GO:query 624s @SQ SN:0 LN:16 624s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 624s r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 624s (fw:0, sam:1) 624s References: 624s >0 624s TTGTTCGTTTGTTCGT 624s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 624s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 624s @HD VN:1.5 SO:unsorted GO:query 624s @SQ SN:0 LN:16 624s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 624s r0 16 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 624s XS:i 1 (fw:1, sam:1) 624s References: 624s >0 624s TTGTTCGATTGTTCGA 624s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 626s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:16 626s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 626s XS:i 1 (fw:0, sam:1) 626s References: 626s >0 626s TTGTTCGATTGTTCGA 626s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:16 626s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 626s XS:i 2 (fw:1, sam:1) 626s References: 626s >0 626s TTGTTCGATTGTTCGA 626s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:16 626s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s r0 4 * 0 0 * * 0 0 TTGTTCGT IIIIIIII YT:Z:UU 626s XS:i 2 (fw:0, sam:1) 626s References: 626s >0 626s TTGTTCGATTGTTCGA 626s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:16 626s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s r0 4 * 0 0 * * 0 0 ACGAACAA IIIIIIII YT:Z:UU 626s XS:i 3a (fw:1, sam:1) 626s References: 626s >0 626s TTGTTCGATTGTTCGT 626s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 626s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:16 626s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 626s XS:i 3a (fw:0, sam:1) 626s References: 626s >0 626s TTGTTCGATTGTTCGT 626s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:16 626s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 626s XS:i 3b (fw:1, sam:1) 626s References: 626s >0 626s TTGTTCGATTGTTCGT 626s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 626s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 626s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 626s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:16 626s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 626s XS:i 3b (fw:0, sam:1) 626s References: 626s >0 626s TTGTTCGATTGTTCGT 626s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:16 626s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 626s XS:i 3c (fw:1, sam:1) 626s References: 626s >0 626s TTGTTCGATTGTTCGT 626s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:16 626s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 626s XS:i 3c (fw:0, sam:1) 626s References: 626s >0 626s TTGTTCGATTGTTCGT 626s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 626s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 626s @HD VN:1.5 SO:unsorted GO:query 626s @SQ SN:0 LN:16 626s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 626s r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 626s XS:i 4a (fw:1, sam:1) 626s References: 626s >0 626s TTGTTCAATTGTTCGATTGTTCGT 626s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 626s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 627s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 627s @HD VN:1.5 SO:unsorted GO:query 627s @SQ SN:0 LN:24 627s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 627s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 627s XS:i 4a (fw:0, sam:1) 627s References: 627s >0 627s TTGTTCAATTGTTCGATTGTTCGT 627s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 627s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 627s @HD VN:1.5 SO:unsorted GO:query 627s @SQ SN:0 LN:24 627s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 627s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 627s XS:i 4b (fw:1, sam:1) 627s References: 627s >0 627s TTGTTCAATTGTTCGATTGTTCGT 627s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 627s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 627s @HD VN:1.5 SO:unsorted GO:query 627s @SQ SN:0 LN:24 627s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 627s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 627s XS:i 4b (fw:0, sam:1) 627s References: 627s >0 627s TTGTTCAATTGTTCGATTGTTCGT 627s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 627s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 627s @HD VN:1.5 SO:unsorted GO:query 627s @SQ SN:0 LN:24 627s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 627s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 627s XS:i 5a (fw:1, sam:1) 627s References: 627s >0 627s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 627s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 627s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 627s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 627s @HD VN:1.5 SO:unsorted GO:query 627s @SQ SN:0 LN:120 627s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 627s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 628s XS:i 5a (fw:0, sam:1) 628s References: 628s >0 628s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 628s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 628s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 628s @HD VN:1.5 SO:unsorted GO:query 628s @SQ SN:0 LN:120 628s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 628s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 628s XS:i 5b (fw:1, sam:1) 628s References: 628s >0 628s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 628s /usr/bin/bowtie2 --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 628s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 628s @HD VN:1.5 SO:unsorted GO:query 628s @SQ SN:0 LN:120 628s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 628s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 628s XS:i 5b (fw:0, sam:1) 628s References: 628s >0 628s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 628s /usr/bin/bowtie2 --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 628s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 628s @HD VN:1.5 SO:unsorted GO:query 628s @SQ SN:0 LN:120 628s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 628s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 628s BWA-SW-like 1 (fw:1, sam:1) 628s References: 628s >0 628s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 628s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 628s /usr/bin/bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 628s @HD VN:1.5 SO:unsorted GO:query 628s @SQ SN:0 LN:64 628s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 628s r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU 628s BWA-SW-like 1 (fw:0, sam:1) 628s References: 628s >0 628s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 628s /usr/bin/bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 628s @HD VN:1.5 SO:unsorted GO:query 628s @SQ SN:0 LN:64 628s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 628s r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU 628s BWA-SW-like 2 (fw:1, sam:1) 628s References: 628s >0 628s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 628s /usr/bin/bowtie2 --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 628s @HD VN:1.5 SO:unsorted GO:query 628s @SQ SN:0 LN:64 628s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 628s r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU 628s BWA-SW-like 2 (fw:0, sam:1) 628s References: 628s >0 628s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 628s /usr/bin/bowtie2 --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 628s @HD VN:1.5 SO:unsorted GO:query 628s @SQ SN:0 LN:64 628s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 628s r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU 628s BWA-SW-like 3 (fw:1, sam:1) 628s References: 628s >0 628s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 628s /usr/bin/bowtie2 --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 628s @HD VN:1.5 SO:unsorted GO:query 628s @SQ SN:0 LN:64 628s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 628s r0 0 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU 628s BWA-SW-like 3 (fw:0, sam:1) 628s References: 628s >0 628s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 628s /usr/bin/bowtie2 --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 628s @HD VN:1.5 SO:unsorted GO:query 628s @SQ SN:0 LN:64 628s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 628s r0 16 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU 628s SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1) 628s References: 628s >0 628s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 628s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 629s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 629s @HD VN:1.5 SO:unsorted GO:query 629s @SQ SN:0 LN:69 629s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 629s r0 99 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 629s r0 147 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 629s SAM paired-end where both alignments start at the same offset (ff case) (fw:1, sam:1) 629s References: 629s >0 629s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 629s /usr/bin/bowtie2 --large-index --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 629s @HD VN:1.5 SO:unsorted GO:query 629s @SQ SN:0 LN:69 629s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 629s r0 67 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 629s r0 131 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 629s SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1) 629s References: 629s >0 629s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 629s /usr/bin/bowtie2 --large-index --rf --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 629s @HD VN:1.5 SO:unsorted GO:query 629s @SQ SN:0 LN:69 629s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 629s r0 83 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 629s r0 163 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 629s SAM paired-end where both mates align 1 (fw:1, sam:1) 629s References: 629s >0 629s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 629s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 629s @HD VN:1.5 SO:unsorted GO:query 629s @SQ SN:0 LN:69 629s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 629s r0 99 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP 629s r0 147 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP 629s SAM paired-end where both mates align 2 (fw:1, sam:1) 629s References: 629s >0 629s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 629s /usr/bin/bowtie2 --large-index --rf --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 629s @HD VN:1.5 SO:unsorted GO:query 629s @SQ SN:0 LN:69 629s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 629s r0 83 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP 629s r0 163 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP 629s SAM paired-end where both mates align 3 (fw:1, sam:1) 629s References: 629s >0 629s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 629s /usr/bin/bowtie2 --large-index --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 630s @HD VN:1.5 SO:unsorted GO:query 630s @SQ SN:0 LN:69 630s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 630s r0 67 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP 630s r0 131 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP 630s SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1) 630s References: 630s >0 630s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 630s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 630s @HD VN:1.5 SO:unsorted GO:query 630s @SQ SN:0 LN:69 630s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 630s r0 73 0 4 255 24M = 4 0 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YT:Z:UP 630s r0 133 0 4 0 * = 4 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 630s SAM paired-end where neither mate aligns (fw:1, sam:1) 630s References: 630s >0 630s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 630s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 630s @HD VN:1.5 SO:unsorted GO:query 630s @SQ SN:0 LN:69 630s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 630s r0 77 * 0 0 * * 0 0 CTATATACGAAAAAGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 630s r0 141 * 0 0 * * 0 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 630s SAM paired-end where both mates align, but discordantly (fw:1, sam:1) 630s References: 630s >0 630s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 630s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 630s @HD VN:1.5 SO:unsorted GO:query 630s @SQ SN:0 LN:69 630s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 630s r0 65 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YS:i:0 YT:Z:DP 630s r0 129 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP 630s matchesRef regression 4 (fw:1, sam:1) 630s References: 630s >0 630s CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC 630s >1 630s GCTCGGAATTCGTGCTCCGNCCCGTACGGTT 630s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 630s /usr/bin/bowtie2 --large-index --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 630s @HD VN:1.5 SO:unsorted GO:query 630s @SQ SN:0 LN:120 630s @SQ SN:1 LN:31 630s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 630s r0 4 * 0 0 * * 0 0 ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU 630s matchesRef regression 4 (fw:0, sam:1) 630s References: 630s >0 630s CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC 630s >1 630s GCTCGGAATTCGTGCTCCGNCCCGTACGGTT 630s /usr/bin/bowtie2 --large-index --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 630s @HD VN:1.5 SO:unsorted GO:query 630s @SQ SN:0 LN:120 630s @SQ SN:1 LN:31 630s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 630s r0 4 * 0 0 * * 0 0 GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU 630s matchesRef regression 3 (fw:1, sam:1) 630s References: 630s >0 630s GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC 630s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 630s /usr/bin/bowtie2 --large-index --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 630s @HD VN:1.5 SO:unsorted GO:query 630s @SQ SN:0 LN:53 630s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 630s r0 16 0 10 255 38M * 0 0 CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UU 630s matchesRef regression 3 (fw:0, sam:1) 630s References: 630s >0 630s GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC 630s /usr/bin/bowtie2 --large-index --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 631s @HD VN:1.5 SO:unsorted GO:query 631s @SQ SN:0 LN:53 631s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 631s r0 0 0 10 255 38M * 0 0 CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UU 631s matchesRef regression 2 (fw:1, sam:1) 631s References: 631s >0 631s GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG 631s >1 631s CCTTGTTNTTAATGCTGCCTGGTTTNG 631s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 631s /usr/bin/bowtie2 --large-index --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 631s @HD VN:1.5 SO:unsorted GO:query 631s @SQ SN:0 LN:47 631s @SQ SN:1 LN:27 631s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 631s r0 77 * 0 0 * * 0 0 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 631s r0 141 * 0 0 * * 0 0 ACATATCCAGAGCTGCCGACAACGAAATGAACCCGAGAGCACAAATCCAGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 631s matchesRef regression 2 (fw:0, sam:1) 631s References: 631s >0 631s GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG 631s >1 631s CCTTGTTNTTAATGCTGCCTGGTTTNG 631s /usr/bin/bowtie2 --large-index --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 631s @HD VN:1.5 SO:unsorted GO:query 631s @SQ SN:0 LN:47 631s @SQ SN:1 LN:27 631s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 631s r0 83 0 1 255 29S23M = 1 -68 CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-78 XN:i:7 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:-128 YT:Z:CP 631s r0 163 0 1 255 45S15M = 1 68 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-128 XN:i:9 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:14T0 YS:i:-78 YT:Z:CP 631s matchesRef regression 1 (fw:1, sam:1) 631s References: 631s >0 631s AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC 631s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 631s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 631s @HD VN:1.5 SO:unsorted GO:query 631s @SQ SN:0 LN:61 631s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 631s r0 0 0 12 255 50M10S * 0 0 AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:9 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU 631s matchesRef regression 1 (fw:0, sam:1) 631s References: 631s >0 631s AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC 631s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 631s @HD VN:1.5 SO:unsorted GO:query 631s @SQ SN:0 LN:61 631s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 631s r0 16 0 12 255 50M10S * 0 0 AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:9 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU 631s Discordant with different chromosomes (fw:1, sam:1) 631s References: 631s >0 631s TTTATAAAAATATTTCCCCCCCC 631s >1 631s CCCCCCTGTCGCTACCGCCCCCCCCCCC 631s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 632s /usr/bin/bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 632s @HD VN:1.5 SO:unsorted GO:query 632s @SQ SN:0 LN:23 632s @SQ SN:1 LN:28 632s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 632s r0 65 0 4 255 10M 1 8 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 632s r0 129 1 8 255 10M 0 4 0 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 632s r1 65 0 4 255 10M 1 7 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 632s r1 129 1 7 255 10M 0 4 0 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 632s Discordant with different chromosomes (fw:0, sam:1) 632s References: 632s >0 632s TTTATAAAAATATTTCCCCCCCC 632s >1 632s CCCCCCTGTCGCTACCGCCCCCCCCCCC 632s /usr/bin/bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 632s @HD VN:1.5 SO:unsorted GO:query 632s @SQ SN:0 LN:23 632s @SQ SN:1 LN:28 632s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 632s r0 113 1 8 255 10M 0 4 0 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 632s r0 177 0 4 255 10M 1 8 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 632s r1 113 1 7 255 10M 0 4 0 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 632s r1 177 0 4 255 10M 1 7 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 632s (fw:1, sam:1) 632s References: 632s >0 632s AGCATCGATCAGTATCTGA 632s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 632s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 632s @HD VN:1.5 SO:unsorted GO:query 632s @SQ SN:0 LN:19 632s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 632s r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 632s (fw:0, sam:1) 632s References: 632s >0 632s AGCATCGATCAGTATCTGA 632s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 632s @HD VN:1.5 SO:unsorted GO:query 632s @SQ SN:0 LN:19 632s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 632s r1 16 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 632s (fw:1, sam:1) 632s References: 632s >0 632s AGCATCGATCAGTATCTGA 632s /usr/bin/bowtie2 --large-index -s 1 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:19 633s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 633s r1 99 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 633s r1 147 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 633s (fw:0, sam:1) 633s References: 633s >0 633s AGCATCGATCAGTATCTGA 633s /usr/bin/bowtie2 --large-index -s 1 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:19 633s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 633s r1 83 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 633s r1 163 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 633s (fw:1, sam:1) 633s References: 633s >0 633s AGCATCGATCAGTATCTGA 633s /usr/bin/bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:19 633s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 633s (fw:0, sam:1) 633s References: 633s >0 633s AGCATCGATCAGTATCTGA 633s /usr/bin/bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:19 633s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 633s (fw:1, sam:1) 633s References: 633s >0 633s AGCATCGATCAGTATCTGA 633s /usr/bin/bowtie2 --large-index -s 2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:19 633s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 633s (fw:0, sam:1) 633s References: 633s >0 633s AGCATCGATCAGTATCTGA 633s /usr/bin/bowtie2 --large-index -s 2 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:19 633s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 633s (fw:1, sam:1) 633s References: 633s >0 633s AGCATCGATCAGTATCTGA 633s /usr/bin/bowtie2 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:19 633s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 633s r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 633s (fw:0, sam:1) 633s References: 633s >0 633s AGCATCGATCAGTATCTGA 633s /usr/bin/bowtie2 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:19 633s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 633s r1 16 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 633s (fw:1, sam:1) 633s References: 633s >0 633s AGCATCGATCAGTATCTGA 633s /usr/bin/bowtie2 --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:19 633s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 633s r1 0 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 633s (fw:0, sam:1) 633s References: 633s >0 633s AGCATCGATCAGTATCTGA 633s /usr/bin/bowtie2 --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:19 633s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 633s r1 16 0 6 255 9M * 0 0 CGATCAGTA IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 633s (fw:0, sam:1) 633s References: 633s >0 633s AGCATCGATCAGTATCTGA 633s /usr/bin/bowtie2 --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:19 633s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 633s r1 16 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 633s (fw:1, sam:1) 633s References: 633s >0 633s AGCATCGATCAGTATCTGA 633s /usr/bin/bowtie2 --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 633s @HD VN:1.5 SO:unsorted GO:query 633s @SQ SN:0 LN:19 633s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 633s r1 0 0 6 255 9M * 0 0 CGATCAGTA IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 633s (fw:1, sam:1) 633s References: 633s >0 633s TGC 633s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 633s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 634s @HD VN:1.5 SO:unsorted GO:query 634s @SQ SN:0 LN:3 634s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 634s r0 0 0 1 255 1S3M * 0 0 ATGC IIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 634s (fw:0, sam:1) 634s References: 634s >0 634s TGC 634s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 634s @HD VN:1.5 SO:unsorted GO:query 634s @SQ SN:0 LN:3 634s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 634s r0 16 0 1 255 1S3M * 0 0 ATGC IIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 634s (fw:1, sam:1) 634s References: 634s >0 634s TTGTTCGT 634s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 634s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 634s @HD VN:1.5 SO:unsorted GO:query 634s @SQ SN:0 LN:8 634s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 634s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 634s (fw:0, sam:1) 634s References: 634s >0 634s TTGTTCGT 634s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 634s @HD VN:1.5 SO:unsorted GO:query 634s @SQ SN:0 LN:8 634s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 634s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 634s (fw:1, sam:1) 634s References: 634s >0 634s TTGTTCGT 634s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 634s @HD VN:1.5 SO:unsorted GO:query 634s @SQ SN:0 LN:8 634s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 634s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 634s (fw:0, sam:1) 634s References: 634s >0 634s TTGTTCGT 634s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 634s @HD VN:1.5 SO:unsorted GO:query 634s @SQ SN:0 LN:8 634s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 634s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 634s (fw:1, sam:1) 634s References: 634s >0 634s TTGTTCGT 634s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 634s @HD VN:1.5 SO:unsorted GO:query 634s @SQ SN:0 LN:8 634s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 634s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 634s r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 634s (fw:0, sam:1) 634s References: 634s >0 634s TTGTTCGT 634s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 634s @HD VN:1.5 SO:unsorted GO:query 634s @SQ SN:0 LN:8 634s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 634s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 634s r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 634s (fw:1, sam:1) 634s References: 634s >0 634s TTGTTCGT 634s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 634s @HD VN:1.5 SO:unsorted GO:query 634s @SQ SN:0 LN:8 634s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 634s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 634s r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 634s (fw:0, sam:1) 634s References: 634s >0 634s TTGTTCGT 634s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 635s @HD VN:1.5 SO:unsorted GO:query 635s @SQ SN:0 LN:8 635s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 635s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 635s r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 635s (fw:1, sam:1) 635s References: 635s >0 635s TTGTTCGT 635s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 635s @HD VN:1.5 SO:unsorted GO:query 635s @SQ SN:0 LN:8 635s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 635s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 635s r1 0 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 635s r2 0 0 1 255 1S6M * 0 0 ATTGTTC IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 635s (fw:0, sam:1) 635s References: 635s >0 635s TTGTTCGT 635s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 635s @HD VN:1.5 SO:unsorted GO:query 635s @SQ SN:0 LN:8 635s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 635s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 635s r1 16 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 635s r2 16 0 1 255 1S6M * 0 0 ATTGTTC IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 635s (fw:1, sam:1) 635s References: 635s >0 635s TTGTTCGT 635s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz 635s @HD VN:1.5 SO:unsorted GO:query 635s @SQ SN:0 LN:8 635s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" 635s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 635s r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 635s r2 4 * 0 0 * * 0 0 GTTCGTA IIIIIII YT:Z:UU 635s r3 4 * 0 0 * * 0 0 ATTGTTC IIIIIII YT:Z:UU 635s (fw:0, sam:1) 635s References: 635s >0 635s TTGTTCGT 635s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz 635s @HD VN:1.5 SO:unsorted GO:query 635s @SQ SN:0 LN:8 635s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" 635s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 635s r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 635s r2 4 * 0 0 * * 0 0 TACGAAC IIIIIII YT:Z:UU 635s r3 4 * 0 0 * * 0 0 GAACAAT IIIIIII YT:Z:UU 635s (fw:1, sam:1) 635s References: 635s >0 635s TTGTTCGT 635s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 635s @HD VN:1.5 SO:unsorted GO:query 635s @SQ SN:0 LN:8 635s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 635s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 635s (fw:0, sam:1) 635s References: 635s >0 635s TTGTTCGT 635s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 635s @HD VN:1.5 SO:unsorted GO:query 635s @SQ SN:0 LN:8 635s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 635s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 635s (fw:1, sam:1) 635s References: 635s >0 635s TTGTTCGT 635s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 635s @HD VN:1.5 SO:unsorted GO:query 635s @SQ SN:0 LN:8 635s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 635s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 635s (fw:0, sam:1) 635s References: 635s >0 635s TTGTTCGT 635s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 636s @HD VN:1.5 SO:unsorted GO:query 636s @SQ SN:0 LN:8 636s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 636s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 636s P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) 636s References: 636s >0 636s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 636s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 636s /usr/bin/bowtie2 --large-index -X 1000 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 636s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 636s @HD VN:1.5 SO:unsorted GO:query 636s @SQ SN:0 LN:1000 636s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 636s r0 99 0 13 1 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 636s r0 147 0 961 1 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 636s P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) 636s References: 636s >0 636s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 636s /usr/bin/bowtie2 --large-index -X 1000 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 636s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 636s @HD VN:1.5 SO:unsorted GO:query 636s @SQ SN:0 LN:1000 636s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 636s r0 83 0 961 1 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 636s r0 163 0 13 1 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 636s P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) 636s References: 636s >0 636s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 636s /usr/bin/bowtie2 --large-index -X 1000 --local --fr --quiet -M 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 636s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 636s @HD VN:1.5 SO:unsorted GO:query 636s @SQ SN:0 LN:1000 636s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 636s r0 99 0 13 1 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 636s r0 147 0 961 1 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 636s P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1) 636s References: 636s >0 636s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 636s /usr/bin/bowtie2 --large-index -X 1000 --local --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 636s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 636s @HD VN:1.5 SO:unsorted GO:query 636s @SQ SN:0 LN:1000 636s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 636s r0 83 0 961 1 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 636s r0 163 0 13 1 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 636s P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) 636s References: 636s >0 636s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 636s /usr/bin/bowtie2 --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 636s @HD VN:1.5 SO:unsorted GO:query 636s @SQ SN:0 LN:1000 636s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 636s r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 636s r0 147 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 636s r0 355 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 636s r0 403 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 636s r0 355 0 13 255 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 636s r0 403 0 553 255 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 636s r0 355 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 636s r0 403 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 636s r0 355 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 636s r0 403 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 636s P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) 636s References: 636s >0 636s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 636s /usr/bin/bowtie2 --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 636s @HD VN:1.5 SO:unsorted GO:query 636s @SQ SN:0 LN:1000 636s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 636s r0 83 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 636s r0 163 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 636s r0 339 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 636s r0 419 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 636s r0 339 0 553 255 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 636s r0 419 0 13 255 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 636s r0 339 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 636s r0 419 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 636s r0 339 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 636s r0 419 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 636s P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) 636s References: 636s >0 636s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 636s /usr/bin/bowtie2 --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 636s @HD VN:1.5 SO:unsorted GO:query 636s @SQ SN:0 LN:1000 636s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 636s r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 636s r0 147 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 636s r0 355 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 636s r0 403 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 636s r0 355 0 13 255 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 636s r0 403 0 553 255 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 636s r0 355 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 636s r0 403 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 636s r0 355 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 636s r0 403 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 636s P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1) 636s References: 636s >0 636s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 636s /usr/bin/bowtie2 --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 636s @HD VN:1.5 SO:unsorted GO:query 636s @SQ SN:0 LN:1000 636s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 636s r0 83 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 636s r0 163 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 636s r0 339 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 636s r0 419 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 636s r0 339 0 553 255 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 636s r0 419 0 13 255 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 636s r0 339 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 636s r0 419 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 636s r0 339 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 636s r0 419 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 636s P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 636s References: 636s >0 636s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 636s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 637s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 637s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 637s @HD VN:1.5 SO:unsorted GO:query 637s @SQ SN:0 LN:363 637s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 637s r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 637s r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 637s P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 637s References: 637s >0 637s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 637s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 637s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 637s @HD VN:1.5 SO:unsorted GO:query 637s @SQ SN:0 LN:363 637s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 637s r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 637s r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 637s P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 637s References: 637s >0 637s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 637s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 637s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 637s @HD VN:1.5 SO:unsorted GO:query 637s @SQ SN:0 LN:363 637s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 637s r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 637s r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 637s P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 637s References: 637s >0 637s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 637s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 637s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 637s @HD VN:1.5 SO:unsorted GO:query 637s @SQ SN:0 LN:363 637s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 637s r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 637s r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 637s P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 637s References: 637s >0 637s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 637s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 637s @HD VN:1.5 SO:unsorted GO:query 637s @SQ SN:0 LN:363 637s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 637s r0 99 0 250 255 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 637s r0 147 0 316 255 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 637s P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 637s References: 637s >0 637s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 637s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 637s @HD VN:1.5 SO:unsorted GO:query 637s @SQ SN:0 LN:363 637s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 637s r0 83 0 316 255 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 637s r0 163 0 250 255 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 637s P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 637s References: 637s >0 637s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 637s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 637s @HD VN:1.5 SO:unsorted GO:query 637s @SQ SN:0 LN:363 637s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 637s r0 99 0 250 255 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 637s r0 147 0 316 255 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 637s P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 637s References: 637s >0 637s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 637s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 637s @HD VN:1.5 SO:unsorted GO:query 637s @SQ SN:0 LN:363 637s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 637s r0 83 0 316 255 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 637s r0 163 0 250 255 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 637s P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 637s References: 637s >0 637s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 637s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 637s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 637s @HD VN:1.5 SO:unsorted GO:query 637s @SQ SN:0 LN:363 637s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 637s r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 637s r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 637s P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 637s References: 637s >0 637s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 637s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 -X 150 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 638s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 638s @HD VN:1.5 SO:unsorted GO:query 638s @SQ SN:0 LN:363 638s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 638s r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 638s r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 638s P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 638s References: 638s >0 638s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 638s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 --local -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 638s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 638s @HD VN:1.5 SO:unsorted GO:query 638s @SQ SN:0 LN:363 638s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 638s r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 638s r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 638s P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 638s References: 638s >0 638s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 638s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 --local -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 638s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 638s @HD VN:1.5 SO:unsorted GO:query 638s @SQ SN:0 LN:363 638s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 638s r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 638s r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 638s P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) 638s References: 638s >0 638s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 638s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 638s /usr/bin/bowtie2 --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 638s @HD VN:1.5 SO:unsorted GO:query 638s @SQ SN:0 LN:126 638s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 638s r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 638s r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 638s P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) 638s References: 638s >0 638s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 638s /usr/bin/bowtie2 --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 639s @HD VN:1.5 SO:unsorted GO:query 639s @SQ SN:0 LN:126 639s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 639s r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 639s r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 639s P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) 639s References: 639s >0 639s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 639s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 639s @HD VN:1.5 SO:unsorted GO:query 639s @SQ SN:0 LN:126 639s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 639s r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 639s r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 639s P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) 639s References: 639s >0 639s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 639s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 639s @HD VN:1.5 SO:unsorted GO:query 639s @SQ SN:0 LN:126 639s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 639s r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 639s r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 639s P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) 639s References: 639s >0 639s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 639s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 639s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 639s @HD VN:1.5 SO:unsorted GO:query 639s @SQ SN:0 LN:126 639s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 639s r0 99 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 639s r0 147 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 639s P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) 639s References: 639s >0 639s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 639s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 639s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 639s @HD VN:1.5 SO:unsorted GO:query 639s @SQ SN:0 LN:126 639s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 639s r0 83 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 639s r0 163 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 639s P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) 639s References: 639s >0 639s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 639s /usr/bin/bowtie2 --large-index -X 150 --local --fr --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 639s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 639s @HD VN:1.5 SO:unsorted GO:query 639s @SQ SN:0 LN:126 639s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 639s r0 99 0 13 44 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 639s r0 147 0 79 44 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 639s P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) 639s References: 639s >0 639s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 639s /usr/bin/bowtie2 --large-index -X 150 --local --fr --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 639s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 639s @HD VN:1.5 SO:unsorted GO:query 639s @SQ SN:0 LN:126 639s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 639s r0 83 0 79 44 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 639s r0 163 0 13 44 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 639s P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 639s References: 639s >0 639s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA 639s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 640s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 640s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 640s @HD VN:1.5 SO:unsorted GO:query 640s @SQ SN:0 LN:2607 640s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 640s r0 99 0 1909 1 33M = 1975 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 640s r0 147 0 1975 1 28M = 1909 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 640s P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 640s References: 640s >0 640s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA 640s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 640s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 640s @HD VN:1.5 SO:unsorted GO:query 640s @SQ SN:0 LN:2607 640s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 640s r0 83 0 1975 1 28M = 1909 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 640s r0 163 0 1909 1 33M = 1975 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 640s P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:1, sam:1) 640s References: 640s >0 640s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC 640s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 640s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 640s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 640s @HD VN:1.5 SO:unsorted GO:query 640s @SQ SN:0 LN:1906 640s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 640s r0 99 0 1672 1 33M = 1738 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 640s r0 147 0 1738 1 28M = 1672 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 640s P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1) 640s References: 640s >0 640s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC 640s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 640s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 640s @HD VN:1.5 SO:unsorted GO:query 640s @SQ SN:0 LN:1906 640s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 640s r0 83 0 1738 1 28M = 1672 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 640s r0 163 0 1672 1 33M = 1738 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 640s U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1) 640s References: 640s >0 640s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 640s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 640s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 640s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 640s @HD VN:1.5 SO:unsorted GO:query 640s @SQ SN:0 LN:56 640s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 640s r0 0 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 640s U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1) 640s References: 640s >0 640s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 640s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 641s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 641s @HD VN:1.5 SO:unsorted GO:query 641s @SQ SN:0 LN:56 641s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 641s r0 16 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 641s U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1) 641s References: 641s >0 641s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 641s /usr/bin/bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 641s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 641s @HD VN:1.5 SO:unsorted GO:query 641s @SQ SN:0 LN:56 641s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 641s r0 0 0 13 44 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 641s U.M.1.L. Unpaired -M w/ 1 hit local (fw:0, sam:1) 641s References: 641s >0 641s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 641s /usr/bin/bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 641s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 641s @HD VN:1.5 SO:unsorted GO:query 641s @SQ SN:0 LN:56 641s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 641s r0 16 0 13 44 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 641s U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:1, sam:1) 641s References: 641s >0 641s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 641s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 641s @HD VN:1.5 SO:unsorted GO:query 641s @SQ SN:0 LN:56 641s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 641s r0 0 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 641s U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:0, sam:1) 641s References: 641s >0 641s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 641s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 641s @HD VN:1.5 SO:unsorted GO:query 641s @SQ SN:0 LN:56 641s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 641s r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 641s U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1) 641s References: 641s >0 641s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 641s /usr/bin/bowtie2 --large-index --local --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 641s @HD VN:1.5 SO:unsorted GO:query 641s @SQ SN:0 LN:56 641s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 641s r0 0 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 641s U.M.1.L. Unpaired -m w/ 1 hit local (fw:0, sam:1) 641s References: 641s >0 641s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 641s /usr/bin/bowtie2 --large-index --local --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 641s @HD VN:1.5 SO:unsorted GO:query 641s @SQ SN:0 LN:56 641s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 641s r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 641s U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1) 641s References: 641s >0 641s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 641s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 641s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 641s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 642s @HD VN:1.5 SO:unsorted GO:query 642s @SQ SN:0 LN:85 642s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 642s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 642s U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1) 642s References: 642s >0 642s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 642s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 642s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 642s @HD VN:1.5 SO:unsorted GO:query 642s @SQ SN:0 LN:85 642s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 642s r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 642s U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1) 642s References: 642s >0 642s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 642s /usr/bin/bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 642s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 642s @HD VN:1.5 SO:unsorted GO:query 642s @SQ SN:0 LN:85 642s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 642s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 642s U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1) 642s References: 642s >0 642s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 642s /usr/bin/bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 642s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 642s @HD VN:1.5 SO:unsorted GO:query 642s @SQ SN:0 LN:85 642s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 642s r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 642s U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:1, sam:1) 642s References: 642s >0 642s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 642s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 642s @HD VN:1.5 SO:unsorted GO:query 642s @SQ SN:0 LN:85 642s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 642s r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 642s U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1) 642s References: 642s >0 642s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 642s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 642s @HD VN:1.5 SO:unsorted GO:query 642s @SQ SN:0 LN:85 642s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 642s r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 642s U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1) 642s References: 642s >0 642s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 642s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 642s @HD VN:1.5 SO:unsorted GO:query 642s @SQ SN:0 LN:85 642s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 642s r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 642s U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1) 642s References: 642s >0 642s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 642s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 642s @HD VN:1.5 SO:unsorted GO:query 642s @SQ SN:0 LN:85 642s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 642s r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 642s U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1) 642s References: 642s >0 642s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 642s /usr/bin/bowtie2 --large-index --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 642s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 642s @HD VN:1.5 SO:unsorted GO:query 642s @SQ SN:0 LN:85 642s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 642s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 642s U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1) 642s References: 642s >0 642s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 642s /usr/bin/bowtie2 --large-index --quiet -M 2 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 642s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 642s @HD VN:1.5 SO:unsorted GO:query 642s @SQ SN:0 LN:85 642s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 642s r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 642s U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1) 642s References: 642s >0 642s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 642s /usr/bin/bowtie2 --large-index --quiet -M 2 --local --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 643s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 643s @HD VN:1.5 SO:unsorted GO:query 643s @SQ SN:0 LN:85 643s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 643s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 643s U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1) 643s References: 643s >0 643s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 643s /usr/bin/bowtie2 --large-index --quiet -M 2 --local --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 643s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 643s @HD VN:1.5 SO:unsorted GO:query 643s @SQ SN:0 LN:85 643s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 643s r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 643s U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1) 643s References: 643s >0 643s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 643s /usr/bin/bowtie2 --large-index --quiet -k 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 643s @HD VN:1.5 SO:unsorted GO:query 643s @SQ SN:0 LN:85 643s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 643s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 643s r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 643s U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:0, sam:1) 643s References: 643s >0 643s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 643s /usr/bin/bowtie2 --large-index --quiet -k 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 643s @HD VN:1.5 SO:unsorted GO:query 643s @SQ SN:0 LN:85 643s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 643s r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 643s r0 272 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 643s U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1) 643s References: 643s >0 643s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 643s /usr/bin/bowtie2 --large-index --local --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 643s @HD VN:1.5 SO:unsorted GO:query 643s @SQ SN:0 LN:85 643s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 643s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 643s r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 643s U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:0, sam:1) 643s References: 643s >0 643s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 643s /usr/bin/bowtie2 --large-index --local --quiet -k 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 643s @HD VN:1.5 SO:unsorted GO:query 643s @SQ SN:0 LN:85 643s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 643s r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 643s r0 272 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 643s U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 643s References: 643s >0 643s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 643s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 644s /usr/bin/bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 644s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 644s @HD VN:1.5 SO:unsorted GO:query 644s @SQ SN:0 LN:340 644s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 644s r0 0 0 134 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 644s References: 644s >0 644s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 644s /usr/bin/bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 644s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 644s @HD VN:1.5 SO:unsorted GO:query 644s @SQ SN:0 LN:340 644s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 644s r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 644s References: 644s >0 644s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 644s /usr/bin/bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 644s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 644s @HD VN:1.5 SO:unsorted GO:query 644s @SQ SN:0 LN:340 644s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 644s r0 0 0 134 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 644s References: 644s >0 644s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 644s /usr/bin/bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 644s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 644s @HD VN:1.5 SO:unsorted GO:query 644s @SQ SN:0 LN:340 644s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 644s r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1) 644s References: 644s >0 644s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 644s /usr/bin/bowtie2 --large-index --quiet -k 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 644s @HD VN:1.5 SO:unsorted GO:query 644s @SQ SN:0 LN:340 644s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 644s r0 0 0 219 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s r0 256 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s r0 256 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s r0 256 0 92 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:0, sam:1) 644s References: 644s >0 644s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 644s /usr/bin/bowtie2 --large-index --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 644s @HD VN:1.5 SO:unsorted GO:query 644s @SQ SN:0 LN:340 644s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 644s r0 16 0 262 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s r0 272 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s r0 272 0 92 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s r0 272 0 304 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s r0 272 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 644s U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:1, sam:1) 644s References: 644s >0 644s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 644s /usr/bin/bowtie2 --large-index --local --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 645s @HD VN:1.5 SO:unsorted GO:query 645s @SQ SN:0 LN:340 645s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 645s r0 0 0 219 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 645s r0 256 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 645s r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 645s r0 256 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 645s r0 256 0 92 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 645s U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:0, sam:1) 645s References: 645s >0 645s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 645s /usr/bin/bowtie2 --large-index --local --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 645s @HD VN:1.5 SO:unsorted GO:query 645s @SQ SN:0 LN:340 645s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 645s r0 16 0 262 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 645s r0 272 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 645s r0 272 0 92 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 645s r0 272 0 304 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 645s r0 272 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 645s (fw:1, sam:1) 645s References: 645s >0 645s TTGTTCGTTTGTTCGT 645s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 645s /usr/bin/bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 645s @HD VN:1.5 SO:unsorted GO:query 645s @SQ SN:0 LN:16 645s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 645s r0 0 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 645s r0 256 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 645s (fw:0, sam:1) 645s References: 645s >0 645s TTGTTCGTTTGTTCGT 645s /usr/bin/bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 645s @HD VN:1.5 SO:unsorted GO:query 645s @SQ SN:0 LN:16 645s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 645s r0 16 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 645s r0 272 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 645s (fw:1, sam:1) 645s References: 645s >0 645s TTGTTCGTTTGTTCGT 645s /usr/bin/bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 645s @HD VN:1.5 SO:unsorted GO:query 645s @SQ SN:0 LN:16 645s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 645s r0 4 * 0 0 * * 0 0 TTGTTCAT IIIIIIII YT:Z:UU 645s (fw:0, sam:1) 645s References: 645s >0 645s TTGTTCGTTTGTTCGT 645s /usr/bin/bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 645s @HD VN:1.5 SO:unsorted GO:query 645s @SQ SN:0 LN:16 645s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 645s r0 4 * 0 0 * * 0 0 ATGAACAA IIIIIIII YT:Z:UU 645s (fw:1, sam:1) 645s References: 645s >0 645s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 645s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 646s /usr/bin/bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 646s @HD VN:1.5 SO:unsorted GO:query 646s @SQ SN:0 LN:49 646s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 646s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s (fw:0, sam:1) 646s References: 646s >0 646s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 646s /usr/bin/bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 646s @HD VN:1.5 SO:unsorted GO:query 646s @SQ SN:0 LN:49 646s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 646s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 646s Gap penalties 1 (fw:1, sam:1) 646s References: 646s >0 646s TTGTTCGTTTGTTCGT 646s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 646s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 646s @HD VN:1.5 SO:unsorted GO:query 646s @SQ SN:0 LN:16 646s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 646s r0 0 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU 646s Gap penalties 1 (fw:0, sam:1) 646s References: 646s >0 646s TTGTTCGTTTGTTCGT 646s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 646s @HD VN:1.5 SO:unsorted GO:query 646s @SQ SN:0 LN:16 646s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 646s r0 16 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU 646s Gap penalties 2 (fw:1, sam:1) 646s References: 646s >0 646s TTGTTCGTTTGTTCGT 646s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 646s @HD VN:1.5 SO:unsorted GO:query 646s @SQ SN:0 LN:16 646s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 646s r0 4 * 0 0 * * 0 0 TTGTTCTTTGTT IIIIIIIIIIII YT:Z:UU 646s Gap penalties 2 (fw:0, sam:1) 646s References: 646s >0 646s TTGTTCGTTTGTTCGT 646s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 646s @HD VN:1.5 SO:unsorted GO:query 646s @SQ SN:0 LN:16 646s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 646s r0 4 * 0 0 * * 0 0 AACAAAGAACAA IIIIIIIIIIII YT:Z:UU 646s Gap penalties 3 (fw:1, sam:1) 646s References: 646s >0 646s TTGTTCGTTTGTTCGT 646s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 647s @HD VN:1.5 SO:unsorted GO:query 647s @SQ SN:0 LN:16 647s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 647s r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 647s Gap penalties 3 (fw:0, sam:1) 647s References: 647s >0 647s TTGTTCGTTTGTTCGT 647s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 647s @HD VN:1.5 SO:unsorted GO:query 647s @SQ SN:0 LN:16 647s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 647s r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 647s Gap penalties 4 (fw:1, sam:1) 647s References: 647s >0 647s TTGTTCGTTTGTTCGT 647s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 647s @HD VN:1.5 SO:unsorted GO:query 647s @SQ SN:0 LN:16 647s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 647s r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU 647s Gap penalties 4 (fw:0, sam:1) 647s References: 647s >0 647s TTGTTCGTTTGTTCGT 647s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 647s @HD VN:1.5 SO:unsorted GO:query 647s @SQ SN:0 LN:16 647s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 647s r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU 647s Gap penalties 5 (fw:1, sam:1) 647s References: 647s >0 647s TTGTTCGTTTGTTCGT 647s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 647s @HD VN:1.5 SO:unsorted GO:query 647s @SQ SN:0 LN:16 647s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 647s r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU 647s Gap penalties 5 (fw:0, sam:1) 647s References: 647s >0 647s TTGTTCGTTTGTTCGT 647s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 647s @HD VN:1.5 SO:unsorted GO:query 647s @SQ SN:0 LN:16 647s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 647s r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU 647s Gap penalties 6 (fw:1, sam:1) 647s References: 647s >0 647s ATTGTTCGTTTGTTCGTA 647s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 647s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 647s @HD VN:1.5 SO:unsorted GO:query 647s @SQ SN:0 LN:18 647s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 647s r0 0 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU 647s Gap penalties 6 (fw:0, sam:1) 647s References: 647s >0 647s ATTGTTCGTTTGTTCGTA 647s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 647s @HD VN:1.5 SO:unsorted GO:query 647s @SQ SN:0 LN:18 647s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 647s r0 16 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU 647s Gap penalties 7 (fw:1, sam:1) 647s References: 647s >0 647s TTGTTCGTTTGTTCGT 647s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 647s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 647s @HD VN:1.5 SO:unsorted GO:query 647s @SQ SN:0 LN:16 647s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 647s r0 4 * 0 0 * * 0 0 TTGTTGTTTGATTCGT IIIIIIIIIIIIIIII YT:Z:UU 647s Gap penalties 7 (fw:0, sam:1) 647s References: 647s >0 647s TTGTTCGTTTGTTCGT 647s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 648s @HD VN:1.5 SO:unsorted GO:query 648s @SQ SN:0 LN:16 648s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 648s r0 4 * 0 0 * * 0 0 ACGAATCAAACAACAA IIIIIIIIIIIIIIII YT:Z:UU 648s N filtering 1 (fw:1, sam:1) 648s References: 648s >0 648s GAGACTTTATACGCATCGAACTATCGCTCTA 648s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 648s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 648s @HD VN:1.5 SO:unsorted GO:query 648s @SQ SN:0 LN:31 648s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 648s r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 648s N filtering 1 (fw:0, sam:1) 648s References: 648s >0 648s GAGACTTTATACGCATCGAACTATCGCTCTA 648s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 648s @HD VN:1.5 SO:unsorted GO:query 648s @SQ SN:0 LN:31 648s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 648s r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 648s N filtering 2 (fw:1, sam:1) 648s References: 648s >0 648s GAGACTTTATNCGCATCGAACTATCGCTCTA 648s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 648s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 648s @HD VN:1.5 SO:unsorted GO:query 648s @SQ SN:0 LN:31 648s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 648s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 648s N filtering 2 (fw:0, sam:1) 648s References: 648s >0 648s GAGACTTTATNCGCATCGAACTATCGCTCTA 648s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 648s @HD VN:1.5 SO:unsorted GO:query 648s @SQ SN:0 LN:31 648s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 648s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 648s N filtering 3 (fw:1, sam:1) 648s References: 648s >0 648s GAGACTTTATACGCATCGAANTATCGCTCTA 648s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 649s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 649s @HD VN:1.5 SO:unsorted GO:query 649s @SQ SN:0 LN:31 649s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 649s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 649s N filtering 3 (fw:0, sam:1) 649s References: 649s >0 649s GAGACTTTATACGCATCGAANTATCGCTCTA 649s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 649s @HD VN:1.5 SO:unsorted GO:query 649s @SQ SN:0 LN:31 649s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 649s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 649s N filtering 4 (fw:1, sam:1) 649s References: 649s >0 649s GAGACTTTNTACGCATCGAACTATCGCTCTA 649s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 649s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 649s @HD VN:1.5 SO:unsorted GO:query 649s @SQ SN:0 LN:31 649s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 649s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 649s N filtering 4 (fw:0, sam:1) 649s References: 649s >0 649s GAGACTTTNTACGCATCGAACTATCGCTCTA 649s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 649s @HD VN:1.5 SO:unsorted GO:query 649s @SQ SN:0 LN:31 649s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 649s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 649s N filtering 5 (fw:1, sam:1) 649s References: 649s >0 649s GAGACTTTATNCGCATCGAACTATCGCTCTA 649s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 649s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 649s @HD VN:1.5 SO:unsorted GO:query 649s @SQ SN:0 LN:31 649s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 649s r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU 649s N filtering 5 (fw:0, sam:1) 649s References: 649s >0 649s GAGACTTTATNCGCATCGAACTATCGCTCTA 649s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 650s @HD VN:1.5 SO:unsorted GO:query 650s @SQ SN:0 LN:31 650s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 650s r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU 650s N filtering 6 (fw:1, sam:1) 650s References: 650s >0 650s GAGACTTTNTACGCATCGAANTATCGCTCTA 650s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 650s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 650s @HD VN:1.5 SO:unsorted GO:query 650s @SQ SN:0 LN:31 650s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 650s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 650s N filtering 6 (fw:0, sam:1) 650s References: 650s >0 650s GAGACTTTNTACGCATCGAANTATCGCTCTA 650s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 650s @HD VN:1.5 SO:unsorted GO:query 650s @SQ SN:0 LN:31 650s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 650s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 650s (fw:1, sam:1) 650s References: 650s >0 650s TTTTGTTCGTTTG 650s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 650s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 650s @HD VN:1.5 SO:unsorted GO:query 650s @SQ SN:0 LN:13 650s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 650s r0 0 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 650s (fw:0, sam:1) 650s References: 650s >0 650s TTTTGTTCGTTTG 650s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 650s @HD VN:1.5 SO:unsorted GO:query 650s @SQ SN:0 LN:13 650s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 650s r0 16 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 650s (fw:1, sam:1) 650s References: 650s >0 650s TTGTTCGTTTGTT 650s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 650s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 650s @HD VN:1.5 SO:unsorted GO:query 650s @SQ SN:0 LN:13 650s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 650s r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 650s (fw:0, sam:1) 650s References: 650s >0 650s TTGTTCGTTTGTT 650s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 651s @HD VN:1.5 SO:unsorted GO:query 651s @SQ SN:0 LN:13 651s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 651s r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 651s (fw:1, sam:1) 651s References: 651s >0 651s ACNCA 651s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 651s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 651s @HD VN:1.5 SO:unsorted GO:query 651s @SQ SN:0 LN:5 651s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 651s r0 0 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 651s (fw:0, sam:1) 651s References: 651s >0 651s ACNCA 651s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 651s @HD VN:1.5 SO:unsorted GO:query 651s @SQ SN:0 LN:5 651s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 651s r0 16 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 651s N ceil = 0, 2 legit hits (1) (fw:1, sam:1) 651s References: 651s >0 651s ACNCA 651s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 651s @HD VN:1.5 SO:unsorted GO:query 651s @SQ SN:0 LN:5 651s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 651s r0 0 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 651s N ceil = 0, 2 legit hits (1) (fw:0, sam:1) 651s References: 651s >0 651s ACNCA 651s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 651s @HD VN:1.5 SO:unsorted GO:query 651s @SQ SN:0 LN:5 651s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 651s r0 16 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 651s N ceil = 0, 2 legit hits (2) (fw:1, sam:1) 651s References: 651s >0 651s ACNCANNNNNNNNCGNNNNNNNNCG 651s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 651s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 651s @HD VN:1.5 SO:unsorted GO:query 651s @SQ SN:0 LN:25 651s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 651s r0 16 0 24 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 651s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 651s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 651s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 651s N ceil = 0, 2 legit hits (2) (fw:0, sam:1) 651s References: 651s >0 651s ACNCANNNNNNNNCGNNNNNNNNCG 651s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 651s @HD VN:1.5 SO:unsorted GO:query 651s @SQ SN:0 LN:25 651s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 651s r0 16 0 24 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 651s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 651s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 651s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 651s (fw:1, sam:1) 651s References: 651s >0 651s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 651s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 652s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 652s @HD VN:1.5 SO:unsorted GO:query 652s @SQ SN:0 LN:37 652s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 652s r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s (fw:0, sam:1) 652s References: 652s >0 652s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 652s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 652s @HD VN:1.5 SO:unsorted GO:query 652s @SQ SN:0 LN:37 652s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 652s r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s (fw:1, sam:1) 652s References: 652s >0 652s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 652s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 652s @HD VN:1.5 SO:unsorted GO:query 652s @SQ SN:0 LN:37 652s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 652s r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s (fw:0, sam:1) 652s References: 652s >0 652s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 652s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 652s @HD VN:1.5 SO:unsorted GO:query 652s @SQ SN:0 LN:37 652s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 652s r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 652s (fw:1, sam:1) 652s References: 652s >0 652s TTGTTYGT 652s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 652s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 652s @HD VN:1.5 SO:unsorted GO:query 652s @SQ SN:0 LN:8 652s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 652s r0 0 0 1 255 8M * 0 0 TTGTTGGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU 652s r1 0 0 1 255 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU 652s (fw:1, sam:1) 652s References: 652s >0 652s ATAACCTTCG 652s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 653s /usr/bin/bowtie2 --large-index --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 653s @HD VN:1.5 SO:unsorted GO:query 653s @SQ SN:0 LN:10 653s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 653s r0 0 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU 653s (fw:0, sam:1) 653s References: 653s >0 653s ATAACCTTCG 653s /usr/bin/bowtie2 --large-index --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 653s @HD VN:1.5 SO:unsorted GO:query 653s @SQ SN:0 LN:10 653s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 653s r0 16 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU 653s (fw:1, sam:1) 653s References: 653s >0 653s ATATGCCCCATGCCCCCCTCCG 653s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 653s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 653s @HD VN:1.5 SO:unsorted GO:query 653s @SQ SN:0 LN:22 653s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 653s r0 0 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU 653s (fw:1, sam:1) 653s References: 653s >0 653s ATATGCCCCATGCCCCCCTCCG 653s /usr/bin/bowtie2 --large-index --quiet -a --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 654s @HD VN:1.5 SO:unsorted GO:query 654s @SQ SN:0 LN:22 654s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 654s r0 16 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU 654s Simple paired-end 13 (fw:1, sam:1) 654s References: 654s >0 654s TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC 654s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 654s /usr/bin/bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz 654s @HD VN:1.5 SO:unsorted GO:query 654s @SQ SN:0 LN:51 654s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" 654s r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r0 129 0 31 255 10M = 4 -37 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r1 65 0 4 255 10M = 30 36 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r1 129 0 30 255 10M = 4 -36 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r2 67 0 4 255 10M = 29 35 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r2 131 0 29 255 10M = 4 -35 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r3 67 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r3 131 0 28 255 10M = 4 -34 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r4 65 0 5 255 10M = 31 36 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r4 129 0 31 255 10M = 5 -36 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r5 67 0 5 255 10M = 30 35 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r5 131 0 30 255 10M = 5 -35 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r6 67 0 5 255 10M = 29 34 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r6 131 0 29 255 10M = 5 -34 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r7 67 0 5 255 10M = 28 33 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r7 131 0 28 255 10M = 5 -33 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s Simple paired-end 13 (fw:0, sam:1) 654s References: 654s >0 654s TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC 654s /usr/bin/bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz 654s @HD VN:1.5 SO:unsorted GO:query 654s @SQ SN:0 LN:51 654s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" 654s r0 113 0 31 255 10M = 4 -37 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r1 113 0 30 255 10M = 4 -36 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r1 177 0 4 255 10M = 30 36 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r2 115 0 29 255 10M = 4 -35 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r2 179 0 4 255 10M = 29 35 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r3 115 0 28 255 10M = 4 -34 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r3 179 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r4 113 0 31 255 10M = 5 -36 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r4 177 0 5 255 10M = 31 36 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r5 115 0 30 255 10M = 5 -35 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r5 179 0 5 255 10M = 30 35 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r6 115 0 29 255 10M = 5 -34 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r6 179 0 5 255 10M = 29 34 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r7 115 0 28 255 10M = 5 -33 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r7 179 0 5 255 10M = 28 33 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s Simple paired-end 12 (fw:1, sam:1) 654s References: 654s >0 654s TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC 654s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 654s /usr/bin/bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 654s @HD VN:1.5 SO:unsorted GO:query 654s @SQ SN:0 LN:51 654s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 654s r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r0 129 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 654s r1 67 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s r1 131 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 654s Simple paired-end 12 (fw:0, sam:1) 654s References: 654s >0 654s TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC 654s /usr/bin/bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 655s @HD VN:1.5 SO:unsorted GO:query 655s @SQ SN:0 LN:51 655s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 655s r0 113 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 655s r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 655s r1 115 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 655s r1 179 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 655s Simple paired-end 11 (fw:1, sam:1) 655s References: 655s >0 655s TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC 655s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 655s /usr/bin/bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 655s @HD VN:1.5 SO:unsorted GO:query 655s @SQ SN:0 LN:51 655s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 655s r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 655s r0 129 0 31 255 10M = 4 -37 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 655s Simple paired-end 11 (fw:0, sam:1) 655s References: 655s >0 655s TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC 655s /usr/bin/bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 655s @HD VN:1.5 SO:unsorted GO:query 655s @SQ SN:0 LN:51 655s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 655s r0 113 0 31 255 10M = 4 -37 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 655s r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 655s Simple paired-end 10 (fw:1, sam:1) 655s References: 655s >0 655s TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC 655s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 655s /usr/bin/bowtie2 --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 655s @HD VN:1.5 SO:unsorted GO:query 655s @SQ SN:0 LN:41 655s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 655s r0 65 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 655s r0 129 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 655s Simple paired-end 10 (fw:0, sam:1) 655s References: 655s >0 655s TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC 655s /usr/bin/bowtie2 --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 655s @HD VN:1.5 SO:unsorted GO:query 655s @SQ SN:0 LN:41 655s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 655s r0 113 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 655s r0 177 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 655s Simple paired-end 9 (fw:1, sam:1) 655s References: 655s >0 655s CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC 655s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 656s /usr/bin/bowtie2 --large-index -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 656s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 656s @HD VN:1.5 SO:unsorted GO:query 656s @SQ SN:0 LN:81 656s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 656s r0 99 0 4 1 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s r0 147 0 60 1 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s Simple paired-end 9 (fw:0, sam:1) 656s References: 656s >0 656s CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC 656s /usr/bin/bowtie2 --large-index -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 656s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 656s @HD VN:1.5 SO:unsorted GO:query 656s @SQ SN:0 LN:81 656s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 656s r0 83 0 60 1 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s r0 163 0 4 1 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s Simple paired-end 8 (fw:1, sam:1) 656s References: 656s >0 656s CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC 656s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 656s /usr/bin/bowtie2 --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 656s @HD VN:1.5 SO:unsorted GO:query 656s @SQ SN:0 LN:81 656s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 656s r0 99 0 4 1 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s r0 147 0 60 1 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s r0 355 0 38 255 10M = 60 32 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s r0 403 0 60 255 10M = 38 -32 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s r0 355 0 20 255 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s r0 403 0 60 255 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s Simple paired-end 8 (fw:0, sam:1) 656s References: 656s >0 656s CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC 656s /usr/bin/bowtie2 --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 656s @HD VN:1.5 SO:unsorted GO:query 656s @SQ SN:0 LN:81 656s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 656s r0 83 0 60 1 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s r0 163 0 4 1 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s r0 339 0 60 255 10M = 38 -32 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s r0 419 0 38 255 10M = 60 32 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s r0 339 0 60 255 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s r0 419 0 20 255 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 656s Simple paired-end 2; no --no-mixed (fw:0, sam:1) 656s References: 656s >0 656s CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC 656s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 657s /usr/bin/bowtie2 --large-index -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 657s @HD VN:1.5 SO:unsorted GO:query 657s @SQ SN:0 LN:53 657s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 657s r0 153 0 4 255 10M = 4 0 ATATATATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UP 657s r0 101 0 4 0 * = 4 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 657s Simple paired-end 2; --no-mixed (fw:1, sam:1) 657s References: 657s >0 657s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC 657s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 657s /usr/bin/bowtie2 --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 657s @HD VN:1.5 SO:unsorted GO:query 657s @SQ SN:0 LN:53 657s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 657s r0 77 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP 657s r0 141 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 657s Simple paired-end 2; --no-mixed (fw:0, sam:1) 657s References: 657s >0 657s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC 657s /usr/bin/bowtie2 --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 657s @HD VN:1.5 SO:unsorted GO:query 657s @SQ SN:0 LN:53 657s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 657s r0 77 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 657s r0 141 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP 657s Simple paired-end 1 (fw:1, sam:1) 657s References: 657s >0 657s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC 657s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 657s /usr/bin/bowtie2 --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 658s @HD VN:1.5 SO:unsorted GO:query 658s @SQ SN:0 LN:53 658s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 658s r0 67 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 658s r0 131 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 658s Simple paired-end 1 (fw:0, sam:1) 658s References: 658s >0 658s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC 658s /usr/bin/bowtie2 --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 658s @HD VN:1.5 SO:unsorted GO:query 658s @SQ SN:0 LN:53 658s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 658s r0 115 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 658s r0 179 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 658s (fw:1, sam:1) 658s References: 658s >0 658s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 658s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 658s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 658s @HD VN:1.5 SO:unsorted GO:query 658s @SQ SN:0 LN:49 658s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 658s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s (fw:0, sam:1) 658s References: 658s >0 658s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 658s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 658s @HD VN:1.5 SO:unsorted GO:query 658s @SQ SN:0 LN:49 658s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 658s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 658s (fw:1, sam:1) 658s References: 658s >0 658s TTGTTCGTTTGTTCGT 658s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 659s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 659s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:16 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 659s r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 659s (fw:0, sam:1) 659s References: 659s >0 659s TTGTTCGTTTGTTCGT 659s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 659s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:16 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 659s r0 16 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 659s (fw:1, sam:1) 659s References: 659s >0 659s TTGTTCGT 659s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 659s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:8 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 659s r0 0 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 659s (fw:0, sam:1) 659s References: 659s >0 659s TTGTTCGT 659s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:8 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 660s r0 16 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 660s (fw:1, sam:1) 660s References: 660s >0 660s TTGTTCGTTTGTTCGT 660s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 660s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:16 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 660s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 660s (fw:0, sam:1) 660s References: 660s >0 660s TTGTTCGTTTGTTCGT 660s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:16 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 660s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 660s (fw:1, sam:1) 660s References: 660s >0 660s TTGTTCGTTTGTTCGT 660s /usr/bin/bowtie2 --large-index --policy SEED=0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:16 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 660s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 660s (fw:0, sam:1) 660s References: 660s >0 660s TTGTTCGTTTGTTCGT 660s /usr/bin/bowtie2 --large-index --policy SEED=0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:16 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 660s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 660s (fw:1, sam:1) 660s References: 660s >0 660s TTGTTCGTTTGTTCGT 660s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:16 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 660s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 660s (fw:0, sam:1) 660s References: 660s >0 660s TTGTTCGTTTGTTCGT 660s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:16 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 660s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 660s (fw:1, sam:1) 660s References: 660s >0 660s TTGTTCGTTTGTTCGT 660s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:16 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 660s r0 0 0 9 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 660s r0 256 0 1 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 660s r0 256 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU 660s r0 256 0 4 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2C0G1T0T0G0 YT:Z:UU 660s r0 256 0 8 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T0G1T0C0G0 YT:Z:UU 660s r0 256 0 6 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:0C0G0T2G0T1 YT:Z:UU 660s (fw:0, sam:1) 660s References: 660s >0 660s TTGTTCGTTTGTTCGT 660s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 661s @HD VN:1.5 SO:unsorted GO:query 661s @SQ SN:0 LN:16 661s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 661s r0 16 0 1 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 661s r0 272 0 9 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 661s r0 272 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU 661s r0 272 0 6 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:0C0G0T2G0T1 YT:Z:UU 661s r0 272 0 4 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2C0G1T0T0G0 YT:Z:UU 661s r0 272 0 8 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T0G1T0C0G0 YT:Z:UU 661s PASSED 661s Created DNA generator 661s N frac: 0.009 661s IUPAC frac: 0.010 661s AT/ACGT frac: 0.328 661s A/AT frac: 0.269 661s C/CG frac: 0.283 661s Generating 2 references 661s Generated reference 'Sim.pm.1' of untrimmed length 297, trimmed length 65 661s Generated reference 'Sim.pm.2' of untrimmed length 198, trimmed length 78 661s Wrote references to /tmp/Sim.pm.HBgkkIzX.fa 661s A: 18 661s C: 24 661s G: 70 661s H: 2 661s T: 27 661s W: 2 661s Executing: /usr/bin/bowtie2-build --offrate 3 --bmax 34026 --threads 1 --dcv 64 /tmp/Sim.pm.HBgkkIzX.fa /tmp/Sim.pm.HBgkkIzX 661s *** TEST CASE *** 661s Settings: 661s Output files: "/tmp/Sim.pm.HBgkkIzX.*.bt2" 661s Line rate: 6 (line is 64 bytes) 661s Lines per side: 1 (side is 64 bytes) 661s Offset rate: 3 (one in 8) 661s FTable chars: 10 661s Strings: unpacked 661s Max bucket size: 34026 661s Max bucket size, sqrt multiplier: default 661s Max bucket size, len divisor: default 661s Difference-cover sample period: 64 661s Endianness: little 661s Actual local endianness: little 661s Sanity checking: disabled 661s Assertions: disabled 661s Random seed: 0 661s Sizeofs: void*:8, int:4, long:8, size_t:8 661s Input files DNA, FASTA: 661s /tmp/Sim.pm.HBgkkIzX.fa 661s Building a SMALL indexReading reference sizes 661s Time reading reference sizes: 00:00:00 661s Calculating joined length 661s Writing header 661s Reserving space for joined string 661s Joining reference sequences 661s Time to join reference sequences: 00:00:00 661s bmax according to bmax setting: 34026 661s Using parameters --bmax 25520 --dcv 64 661s Doing ahead-of-time memory usage test 661s Passed! Constructing with these parameters: --bmax 25520 --dcv 64 661s Constructing suffix-array element generator 661s Building DifferenceCoverSample 661s Building sPrime 661s Building sPrimeOrder 661s V-Sorting samples 661s V-Sorting samples time: 00:00:00 661s Allocating rank array 661s 661s Ranking v-sort output 661s Ranking v-sort output time: 00:00:00 661s Invoking Larsson-Sadakane on ranks 661s Invoking Larsson-Sadakane on ranks time: 00:00:00 661s Sanity-checking and returning 661s Skipping building samples since text length 139 is less than bucket size: 25520 661s Converting suffix-array elements to index image 661s Allocating ftab, absorbFtab 661s Entering Ebwt loop 661s Getting block 1 of 1 661s No samples; assembling all-inclusive block 661s Sorting block of length 139 for bucket 1 661s (Using difference cover) 661s Sorting block time: 00:00:00 661s Returning block of 140 for bucket 1 661s Exited Ebwt loop 661s fchr[A]: 0 661s fchr[C]: 18 661s fchr[G]: 42 661s fchr[T]: 112 661s fchr[$]: 139 661s Exiting Ebwt::buildToDisk() 661s Returning from initFromVector 661s Wrote 4194611 bytes to primary EBWT file: /tmp/Sim.pm.HBgkkIzX.1.bt2.tmp 661s Wrote 76 bytes to secondary EBWT file: /tmp/Sim.pm.HBgkkIzX.2.bt2.tmp 661s Re-opening _in1 and _in2 as input streams 661s Returning from Ebwt constructor 661s Headers: 661s len: 139 661s bwtLen: 140 661s sz: 35 661s bwtSz: 35 661s lineRate: 6 661s offRate: 3 661s offMask: 0xfffffff8 661s ftabChars: 10 661s eftabLen: 20 661s eftabSz: 80 661s ftabLen: 1048577 661s ftabSz: 4194308 661s offsLen: 18 661s offsSz: 72 661s lineSz: 64 661s sideSz: 64 661s sideBwtSz: 48 661s sideBwtLen: 192 661s numSides: 1 661s numLines: 1 661s ebwtTotLen: 64 661s ebwtTotSz: 64 661s color: 0 661s reverse: 0 661s Total time for call to driver() for forward index: 00:00:00 661s Reading reference sizes 661s Time reading reference sizes: 00:00:00 661s Calculating joined length 661s Writing header 661s Reserving space for joined string 661s Joining reference sequences 661s Time to join reference sequences: 00:00:00 661s Time to reverse reference sequence: 00:00:00 661s bmax according to bmax setting: 34026 661s Using parameters --bmax 25520 --dcv 64 661s Doing ahead-of-time memory usage test 661s Passed! Constructing with these parameters: --bmax 25520 --dcv 64 661s Constructing suffix-array element generator 661s Building DifferenceCoverSample 661s Building sPrime 661s Building sPrimeOrder 661s V-Sorting samples 661s V-Sorting samples time: 00:00:00 661s Allocating rank array 661s Ranking v-sort output 661s Ranking v-sort output time: 00:00:00 661s Invoking Larsson-Sadakane on ranks 661s Invoking Larsson-Sadakane on ranks time: 00:00:00 661s Sanity-checking and returning 661s Skipping building samples since text length 139 is less than bucket size: 25520 661s Converting suffix-array elements to index image 661s Allocating ftab, absorbFtab 661s Entering Ebwt loop 661s Getting block 1 of 1 661s No samples; assembling all-inclusive block 661s Sorting block of length 139 for bucket 1 661s (Using difference cover) 661s Sorting block time: 00:00:00 661s Returning block of 140 for bucket 1 661s Exited Ebwt loop 661s fchr[A]: 0 661s fchr[C]: 18 661s fchr[G]: 42 661s fchr[T]: 112 661s fchr[$]: 139 661s Exiting Ebwt::buildToDisk() 661s Returning from initFromVector 661s Wrote 4194611 bytes to primary EBWT file: /tmp/Sim.pm.HBgkkIzX.rev.1.bt2.tmp 661s Wrote 76 bytes to secondary EBWT file: /tmp/Sim.pm.HBgkkIzX.rev.2.bt2.tmp 661s Re-opening _in1 and _in2 as input streams 661s Returning from Ebwt constructor 661s Headers: 661s len: 139 661s bwtLen: 140 661s sz: 35 661s bwtSz: 35 661s lineRate: 6 661s offRate: 3 661s offMask: 0xfffffff8 661s ftabChars: 10 661s eftabLen: 20 661s eftabSz: 80 661s ftabLen: 1048577 661s ftabSz: 4194308 661s offsLen: 18 661s offsSz: 72 661s lineSz: 64 661s sideSz: 64 661s sideBwtSz: 48 661s sideBwtLen: 192 661s numSides: 1 661s numLines: 1 661s ebwtTotLen: 64 661s ebwtTotSz: 64 661s color: 0 661s reverse: 1 661s Total time for backward call to driver() for mirror index: 00:00:00 661s Renaming /tmp/Sim.pm.HBgkkIzX.3.bt2.tmp to /tmp/Sim.pm.HBgkkIzX.3.bt2 661s Renaming /tmp/Sim.pm.HBgkkIzX.4.bt2.tmp to /tmp/Sim.pm.HBgkkIzX.4.bt2 661s Renaming /tmp/Sim.pm.HBgkkIzX.1.bt2.tmp to /tmp/Sim.pm.HBgkkIzX.1.bt2 661s Renaming /tmp/Sim.pm.HBgkkIzX.2.bt2.tmp to /tmp/Sim.pm.HBgkkIzX.2.bt2 661s Renaming /tmp/Sim.pm.HBgkkIzX.rev.1.bt2.tmp to /tmp/Sim.pm.HBgkkIzX.rev.1.bt2 661s Renaming /tmp/Sim.pm.HBgkkIzX.rev.2.bt2.tmp to /tmp/Sim.pm.HBgkkIzX.rev.2.bt2 661s Built nucleotide index '/tmp/Sim.pm.HBgkkIzX' 661s Flattened IUPAC characters 661s Mutating sequence Sim.pm.2 661s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 661s Finished SNPs 661s Finished ref gaps 661s Finished read gaps 661s Mutating sequence Sim.pm.1 661s Introducing 11 SNPs, 2/5 ref/read gaps, and 0 rearrangements 661s Finished SNPs 661s Finished ref gaps 661s Finished read gaps 661s Mutated reference genome to subject genome 661s SNPs introduced: 21 661s Reference gaps introduced: 2 661s Read gaps introduced: 5 661s Rearrangements introduced: 1 661s Created read sampler 661s Sampling 69 reads 661s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 661s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 661s parsing sequence Sim.pm.1... 661s parsing sequence Sim.pm.2... 661s *** Run 1 of 100 661s /usr/bin/bowtie2 -k 2 --score-min L,3.15101302733464,8.55533160697817 --mm --rfg 7.67295878436486,17.890488977866 --rdg 25.3617356930615,5.24188588585719 --cp-min 2 --np 3 --cp-ival 2 --local -q -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq 661s Parsed 143 reference bases 661s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 661s Warning: skipping read '29' because it was < 2 characters long 661s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 661s Warning: skipping read '33' because it was < 2 characters long 661s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 661s Warning: skipping read '36' because it was < 2 characters long 661s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 661s Warning: skipping read '44' because it was < 2 characters long 661s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 661s Warning: skipping read '68' because it was < 2 characters long 661s 69 reads; of these: 661s 69 (100.00%) were unpaired; of these: 661s 69 (100.00%) aligned 0 times 661s 0 (0.00%) aligned exactly 1 time 661s 0 (0.00%) aligned >1 times 661s 0.00% overall alignment rate 661s Read 50 alignments... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s --- Summary --- 661s /usr/bin/bowtie2 -k 2 --score-min L,3.15101302733464,8.55533160697817 --mm --rfg 7.67295878436486,17.890488977866 --rdg 25.3617356930615,5.24188588585719 --cp-min 2 --np 3 --cp-ival 2 --local -q -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 661s Read 1 reference strings 661s Checked 0 alignments, 0 edits 661s --------------- 661s PASSED 661s ALSO checking that bowtie2 and bowtie2-align match up 661s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 661s Warning: skipping read '29' because it was < 2 characters long 661s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 661s Warning: skipping read '33' because it was < 2 characters long 661s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 661s Warning: skipping read '36' because it was < 2 characters long 661s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 661s Warning: skipping read '44' because it was < 2 characters long 661s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 661s Warning: skipping read '68' because it was < 2 characters long 661s 69 reads; of these: 661s 69 (100.00%) were unpaired; of these: 661s 69 (100.00%) aligned 0 times 661s 0 (0.00%) aligned exactly 1 time 661s 0 (0.00%) aligned >1 times 661s 0.00% overall alignment rate 661s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 661s Flattened IUPAC characters 661s Mutating sequence Sim.pm.1 661s Introducing 0 SNPs, 0/3 ref/read gaps, and 0 rearrangements 661s Finished SNPs 661s Finished ref gaps 661s Finished read gaps 661s Mutating sequence Sim.pm.2 661s Introducing 6 SNPs, 1/1 ref/read gaps, and 0 rearrangements 661s Finished SNPs 661s Finished ref gaps 661s Finished read gaps 661s Mutated reference genome to subject genome 661s SNPs introduced: 6 661s Reference gaps introduced: 1 661s Read gaps introduced: 4 661s Rearrangements introduced: 0 661s Created read sampler 661s Sampling 97 reads 661s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 661s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 661s parsing sequence Sim.pm.1... 661s *** Run 2 of 100 661s /usr/bin/bowtie2 --mm --ma 39.9878452732073 --score-min L,7.87012013604874,4.37510282866831 -k 4 --np 6 --cp-min 5 --rfg 21.888475980852 --trim3 9 -i L,0.14971618481254 --mp 9.77036677742432,9.16017459594405 --cp-ival 1 --norc --trim5 7 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 661s parsing sequence Sim.pm.2... 661s Parsed 143 reference bases 661s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 661s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 661s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 661s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 661s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 661s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 661s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 661s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 661s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 661s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 661s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 661s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 661s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 661s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 661s Read 50 alignments... 661s 97 reads; of these: 661s 57 (58.76%) were paired; of these: 661s 57 (100.00%) aligned concordantly 0 times 661s 0 (0.00%) aligned concordantly exactly 1 time 661s 0 (0.00%) aligned concordantly >1 times 661s ---- 661s 57 pairs aligned concordantly 0 times; of these: 661s 0 (0.00%) aligned discordantly 1 time 661s ---- 661s 57 pairs aligned 0 times concordantly or discordantly; of these: 661s 114 mates make up the pairs; of these: 661s 103 (90.35%) aligned 0 times 661s 3 (2.63%) aligned exactly 1 time 661s 8 (7.02%) aligned >1 times 661s 40 (41.24%) were unpaired; of these: 661s 36 (90.00%) aligned 0 times 661s 1 (2.50%) aligned exactly 1 time 661s 3 (7.50%) aligned >1 times 661s 9.74% overall alignment rate 661s Read 100 alignments... 661s Read 150 alignments... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s GGTGGT 661s GGTGGT 661s Processing line... 661s GGTGGT 661s GGTGGT 661s Processing line... 661s GGTGGT 661s GGTGGT 661s Processing line... 661s GGTGGT 661s GGTGGT 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s AC 661s AC 661s Processing line... 661s AC 661s AC 661s Processing line... 661s AC 661s AC 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s AC 661s AC 661s Processing line... 661s AC 661s AC 661s Processing line... 661s AC 661s AC 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s TCCGGGTGGTGTTG 661s TCCGGGTGGTGTTG 661s Processing line... 661s TCCGGGTGGTGTTG 661s TCCGGGTGGTGTTG 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s GAGG 661s GAGG 661s Processing line... 661s GAGG 661s GAGG 661s Processing line... 661s GAGG 661s GAGG 661s Processing line... 661s GAGG 661s GAGG 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s AA 661s AA 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s CCAGCTTA 661s CCAGCTTA 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s CC 661s CC 661s Processing line... 661s CC 661s CC 661s Processing line... 661s CC 661s CC 661s Processing line... 661s CC 661s CC 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s AG 661s AG 661s Processing line... 661s AG 661s AG 661s Processing line... 661s AG 661s AG 661s Processing line... 661s AG 661s AG 661s Processing line... 661s Processing line... 661s Processing line... 661s GA 661s GA 661s Processing line... 661s GA 661s GA 661s Processing line... 661s GA 661s GA 661s Processing line... 661s GA 661s GA 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s CA 661s CA 661s Processing line... 661s CA 661s CA 661s Processing line... 661s CA 661s CA 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s AGGGGGGGACTGGCGGGA 661s AGGGGGGGACTGGCGGGA 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s GGC 661s GGC 661s Processing line... 661s GGC 661s GGC 661s Processing line... 661s GGC 661s GGC 661s Processing line... 661s GGC 661s GGC 661s Processing line... 661s GTGACAGAGGCGTG 661s GTGACAGAGGCGTG 661s Processing line... 661s Processing line... 661s Processing line... 661s Processing line... 661s /usr/bin/bowtie2 --mm --ma 39.9878452732073 --score-min L,7.87012013604874,4.37510282866831 -k 4 --np 6 --cp-min 5 --rfg 21.888475980852 --trim3 9 -i L,0.14971618481254 --mp 9.77036677742432,9.16017459594405 --cp-ival 1 --norc --trim5 7 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 661s Processing line... 661s Processing line... 661s Processing line... 661s GGGA 661s GGGA 661s Processing line... 661s GGGA 661s GGGA 661s Processing line... 661s GGGA 661s GGGA 661s Processing line... 661s --- Summary --- 661s Read 1 reference strings 661s Checked 42 alignments, 0 edits 661s --------------- 661s PASSED 661s ALSO checking that bowtie2 and bowtie2-align match up 662s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 662s 97 reads; of these: 662s 57 (58.76%) were paired; of these: 662s 57 (100.00%) aligned concordantly 0 times 662s 0 (0.00%) aligned concordantly exactly 1 time 662s 0 (0.00%) aligned concordantly >1 times 662s ---- 662s 57 pairs aligned concordantly 0 times; of these: 662s 0 (0.00%) aligned discordantly 1 time 662s ---- 662s 57 pairs aligned 0 times concordantly or discordantly; of these: 662s 114 mates make up the pairs; of these: 662s 103 (90.35%) aligned 0 times 662s 3 (2.63%) aligned exactly 1 time 662s 8 (7.02%) aligned >1 times 662s 40 (41.24%) were unpaired; of these: 662s 36 (90.00%) aligned 0 times 662s 1 (2.50%) aligned exactly 1 time 662s 3 (7.50%) aligned >1 times 662s 9.74% overall alignment rate 662s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 662s /usr/bin/bowtie2 --mm --ma 39.9878452732073 --score-min L,7.87012013604874,4.37510282866831 -k 4 --np 6 --cp-min 5 --rfg 21.888475980852 --trim3 9 -i L,0.14971618481254 --mp 9.77036677742432,9.16017459594405 --cp-ival 1 --norc --trim5 7 --qseq -p 2 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 662s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 662s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 662s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 662s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 662s 97 reads; of these: 662s 57 (58.76%) were paired; of these: 662s 57 (100.00%) aligned concordantsort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 662s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 662s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 662s ly 0 times 662s 0 (0.00%) aligned concordantly exactly 1 time 662s 0 (0.00%) aligned concordantly >1 times 662s ---- 662s 57 pairs aligned concordantly 0 times; of these: 662s 0 (0.00%) aligned discordantly 1 time 662s ---- 662s 57 pairs aligned 0 times concordantly or discordantly; of these: 662s 114 mates make up the pairs; of these: 662s 103 (90.35%) aligned 0 times 662s 3 (2.63%) aligned exactly 1 time 662s 8 (7.02%) aligned >1 times 662s 40 (41.24%) were unpaired; of these: 662s 36 (90.00%) aligned 0 times 662s 1 (2.50%) aligned exactly 1 time 662s 3 (7.50%) aligned >1 times 662s 9.74% overall alignment rate 662s Flattened IUPAC characters 662s Mutating sequence Sim.pm.2 662s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 662s Finished SNPs 662s Finished ref gaps 662s Finished read gaps 662s Mutating sequence Sim.pm.1 662s Introducing 5 SNPs, 2/1 ref/read gaps, and 0 rearrangements 662s Finished SNPs 662s Finished ref gaps 662s Finished read gaps 662s Mutated reference genome to subject genome 662s SNPs introduced: 5 662s Reference gaps introduced: 3 662s Read gaps introduced: 1 662s Rearrangements introduced: 1 662s *** Run 3 of 100 662s /usr/bin/bowtie2 --trim3 4 --score-min L,3.64644738191181,8.32152694572219 --mp 8.8345682932708,3.41467591060673 --cp-ival 4 --cp-min 3 --trim5 9 --n-ceil 0.757758037377816,0.871824336287132 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 662s Created read sampler 662s Sampling 21 reads 662s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 662s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 662s parsing sequence Sim.pm.1... 662s parsing sequence Sim.pm.2... 662s Parsed 143 reference bases 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 662s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read '1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 662s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 662s Warning: skipping read '6' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 662s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 662s Warning: skipping read '8' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 662s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read '18' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 662s 21 reads; of these: 662s 14 (66.67%) were paired; of these: 662s 14 (100.00%) aligned concordantly 0 times 662s 0 (0.00%) aligned concordantly exactly 1 time 662s 0 (0.00%) aligned concordantly >1 times 662s ---- 662s 14 pairs aligned concordantly 0 times; of these: 662s 0 (0.00%) aligned discordantly 1 time 662s ---- 662s 14 pairs aligned 0 times concordantly or discordantly; of these: 662s 28 mates make up the pairs; of these: 662s 27 (96.43%) aligned 0 times 662s 0 (0.00%) aligned exactly 1 time 662s 1 (3.57%) aligned >1 times 662s 7 (33.33%) were unpaired; of these: 662s 7 (100.00%) aligned 0 times 662s 0 (0.00%) aligned exactly 1 time 662s 0 (0.00%) aligned >1 times 662s 2.86% overall alignment rate 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s CC 662s CC 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s --- Summary --- 662s Read 1 reference strings 662s Checked 1 alignments, 0 edits 662s /usr/bin/bowtie2 --trim3 4 --score-min L,3.64644738191181,8.32152694572219 --mp 8.8345682932708,3.41467591060673 --cp-ival 4 --cp-min 3 --trim5 9 --n-ceil 0.757758037377816,0.871824336287132 -r -p 4 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 662s --------------- 662s PASSED 662s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 662s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read '1' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 662s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 662s Warning: skipping read '6' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 662s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read '18' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 662s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 662s Warning: skipping read '8' because it was < 2 characters long 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 662s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 662s 21 reads; of these: 662s 14 (66.67%) were paired; of these: 662s 14 (100.00%) aligned concordantly 0 times 662s 0 (0.00%) aligned concordantly exactly 1 time 662s 0 (0.00%) aligned concordantly >1 times 662s ---- 662s 14 pairs aligned concordantly 0 times; of these: 662s 0 (0.00%) aligned discordantly 1 time 662s ---- 662s 14 pairs aligned 0 times concordantly or discordantly; of these: 662s 28 mates make up the pairs; of these: 662s 27 (96.43%) aligned 0 times 662s 0 (0.00%) aligned exactly 1 time 662s 1 (3.57%) aligned >1 times 662s 7 (33.33%) were unpaired; of these: 662s 7 (100.00%) aligned 0 times 662s 0 (0.00%) aligned exactly 1 time 662s 0 (0.00%) aligned >1 times 662s 2.86% overall alignment rate 662s Flattened IUPAC characters 662s Mutating sequence Sim.pm.2 662s Introducing 16 SNPs, 1/3 ref/read gaps, and 1 rearrangements 662s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 662s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 662s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 662s Finished SNPs 662s Finished ref gaps 662s Finished read gaps 662s Mutating sequence Sim.pm.1 662s Introducing 9 SNPs, 1/3 ref/read gaps, and 0 rearrangements 662s Finished SNPs 662s Finished ref gaps 662s Finished read gaps 662s Mutated reference genome to subject genome 662s SNPs introduced: 25 662s Reference gaps introduced: 2 662s Read gaps introduced: 6 662s Rearrangements introduced: 1 662s Created read sampler 662s Sampling 106 reads 662s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 662s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 662s parsing sequence Sim.pm.1... 662s parsing sequence Sim.pm.2... 662s Parsed 143 reference bases 662s *** Run 4 of 100 662s /usr/bin/bowtie2 --mm --score-min L,4.70971508013354,4.23087841999934 -R 4 --gbar 6 --cp-min 5 --rfg 48.4650706786341,3.10169693252269 --mp 9.84605045426371,2.43639884474403 --local --cp-ival 1 --n-ceil 0.617129194296888,0.414864087367173 --trim5 5 --norc --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 662s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 662s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 662s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 662s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 662s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 662s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 662s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 662s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 662s Read 50 alignments... 662s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 662s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 662s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 662s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 662s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 662s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 662s 106 reads; of these: 662s 92 (86.79%) were paired; of these: 662s 92 (100.00%) aligned concordantly 0 times 662s 0 (0.00%) aligned concordantly exactly 1 time 662s 0 (0.00%) aligned concordantly >1 times 662s ---- 662s 92 pairs aligned concordantly 0 times; of these: 662s 0 (0.00%) aligned discordantly 1 time 662s ---- 662s 92 pairs aligned 0 times concordantly or discordantly; of these: 662s 184 mates make up the pairs; of these: 662s 184 (100.00%) aligned 0 times 662s 0 (0.00%) aligned exactly 1 time 662s 0 (0.00%) aligned >1 times 662s 14 (13.21%) were unpaired; of these: 662s 14 (100.00%) aligned 0 times 662s 0 (0.00%) aligned exactly 1 time 662s 0 (0.00%) aligned >1 times 662s 0.00% overall alignment rate 662s Read 100 alignments... 662s Read 150 alignments... 662s Read 200 alignments... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s --- Summary --- 662s Read 1 reference strings 662s Checked 0 alignments, 0 edits 662s --------------- 662s PASSED 662s Flattened IUPAC characters 662s Mutating sequence Sim.pm.2 662s Introducing 12 SNPs, 1/0 ref/read gaps, and 1 rearrangements 662s Finished SNPs 662s Finished ref gaps 662s Finished read gaps 662s Mutating sequence Sim.pm.1 662s Introducing 5 SNPs, 0/2 ref/read gaps, and 1 rearrangements 662s Finished SNPs 662s Finished ref gaps 662s Finished read gaps 662s Mutated reference genome to subject genome 662s SNPs introduced: 17 662s Reference gaps introduced: 1 662s Read gaps introduced: 2 662s Rearrangements introduced: 2 662s Created read sampler 662s Sampling 36 reads 662s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 662s *** Run 5 of 100 662s /usr/bin/bowtie2 --score-min L,8.46232040659396,3.81458873080092 -D 8 --mp 6.22000677869682,4.44924733237644 --np 1 --cp-min 6 --local --cp-ival 1 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 662s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 662s parsing sequence Sim.pm.1... 662s parsing sequence Sim.pm.2... 662s Parsed 143 reference bases 662s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read '17' because it was < 2 characters long 662s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 662s Warning: skipping mate #1 of read '27' because it was < 2 characters long 662s 36 reads; of these: 662s 36 (100.00%) were paired; of these: 662s 36 (100.00%) aligned concordantly 0 times 662s 0 (0.00%) aligned concordantly exactly 1 time 662s 0 (0.00%) aligned concordantly >1 times 662s ---- 662s 36 pairs aligned concordantly 0 times; of these: 662s 0 (0.00%) aligned discordantly 1 time 662s ---- 662s 36 pairs aligned 0 times concordantly or discordantly; of these: 662s 72 mates make up the pairs; of these: 662s 72 (100.00%) aligned 0 times 662s 0 (0.00%) aligned exactly 1 time 662s 0 (0.00%) aligned >1 times 662s 0.00% overall alignment rate 662s Read 50 alignments... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s /usr/bin/bowtie2 --score-min L,8.46232040659396,3.81458873080092 -D 8 --mp 6.22000677869682,4.44924733237644 --np 1 --cp-min 6 --local --cp-ival 1 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s Processing line... 662s --- Summary --- 662s Read 1 reference strings 662s Checked 0 alignments, 0 edits 662s --------------- 662s PASSED 662s ALSO checking that bowtie2 and bowtie2-align match up 663s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 663s Warning: skipping mate #1 of read '17' because it was < 2 characters long 663s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 663s Warning: skipping mate #1 of read '27' because it was < 2 characters long 663s 36 reads; of these: 663s 36 (100.00%) were paired; of these: 663s 36 (100.00%) aligned concordantly 0 times 663s 0 (0.00%) aligned concordantly exactly 1 time 663s 0 (0.00%) aligned concordantly >1 times 663s ---- 663s 36 pairs aligned concordantly 0 times; of these: 663s 0 (0.00%) aligned discordantly 1 time 663s ---- 663s 36 pairs aligned 0 times concordantly or discordantly; of these: 663s 72 mates make up the pairs; of these: 663s 72 (100.00%) aligned 0 times 663s 0 (0.00%) aligned exactly 1 time 663s 0 (0.00%) aligned >1 times 663s 0.00% overall alignment rate 663s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 663s Flattened IUPAC characters 663s Mutating sequence Sim.pm.1 663s Introducing 6 SNPs, 1/0 ref/read gaps, and 1 rearrangements 663s Finished SNPs 663s Finished ref gaps 663s Finished read gaps 663s Mutating sequence Sim.pm.2 663s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 663s Finished SNPs 663s Finished ref gaps 663s Finished read gaps 663s Mutated reference genome to subject genome 663s SNPs introduced: 8 663s Reference gaps introduced: 2 663s Read gaps introduced: 0 663s Rearrangements introduced: 1 663s Created read sampler 663s Sampling 76 reads 663s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 663s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 663s parsing sequence Sim.pm.1... 663s *** Run 6 of 100 663s /usr/bin/bowtie2 --cp-min 2 -a --cp-ival 1 --trim3 1 --ma 24.6490870919881 --score-min L,4.52728145840528,7.06411031049182 -N 1 -L29 --rdg 20.3726899822609,2.1357875701701 --mm --rfg 38.1751700993113,14.8540403114601 -q -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq 663s parsing sequence Sim.pm.2... 663s Parsed 143 reference bases 663s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 663s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 663s Warning: skipping read '3' because length (1) <= # seed mismatches (1) 663s Warning: skipping read '3' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 663s Warning: skipping read '9' because length (1) <= # seed mismatches (1) 663s Warning: skipping read '9' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 663s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '14' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 663s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '29' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 663s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '31' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 663s Warning: skipping read '51' because length (1) <= # seed mismatches (1) 663s Warning: skipping read '51' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 663s Read 50 alignments... 663s Read 100 alignments... 663s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 663s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '75' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 663s 76 reads; of these: 663s 76 (100.00%) were unpaired; of these: 663s 62 (81.58%) aligned 0 times 663s 7 (9.21%) aligned exactly 1 time 663s 7 (9.21%) aligned >1 times 663s 18.42% overall alignment rate 663s Read 150 alignments... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s GTG 663s GTG 663s Processing line... 663s GTG 663s GTG 663s Processing line... 663s GTG 663s GTG 663s Processing line... 663s GTG 663s GTG 663s Processing line... 663s GTG 663s GTG 663s Processing line... 663s GTG 663s GTG 663s Processing line... 663s GTG 663s GTG 663s Processing line... 663s GTG 663s GTG 663s Processing line... 663s GTG 663s GTG 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s TCGGTCTGCGCCCAGCTTAGGCG 663s TCGGTCTGCGCCCAGCTTAGGCG 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s GGGGGGACTGGCGGGA 663s GGGGGGACTGGCGGGA 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s AGA 663s AGA 663s Processing line... 663s AGA 663s AGA 663s Processing line... 663s TCT 663s TCT 663s Processing line... 663s AGA 663s AGA 663s Processing line... 663s AGA 663s AGA 663s Processing line... 663s Processing line... 663s Processing line... 663s GCGGTCAGGAGGGA 663s GCGGTCAGGAGGGA 663s Processing line... 663s GGCTCGG 663s GGCTCGG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s CC 663s CC 663s Processing line... 663s GG 663s GG 663s Processing line... 663s CC 663s CC 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s CC 663s CC 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s CC 663s CC 663s Processing line... 663s GG 663s GG 663s Processing line... 663s CC 663s CC 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s AC 663s AC 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s AC 663s AC 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s AC 663s AC 663s Processing line... 663s GT 663s GT 663s Processing line... 663s Processing line... 663s Processing line... 663s TGTTGAGAGG 663s TGTTGAGAGG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s CC 663s CC 663s Processing line... 663s GG 663s GG 663s Processing line... 663s CC 663s CC 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s CC 663s CC 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s /usr/bin/bowtie2 --cp-min 2 -a --cp-ival 1 --trim3 1 --ma 24.6490870919881 --score-min L,4.52728145840528,7.06411031049182 -N 1 -L29 --rdg 20.3726899822609,2.1357875701701 --mm --rfg 38.1751700993113,14.8540403114601 -q -p 3 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s CC 663s CC 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s GG 663s GG 663s Processing line... 663s CC 663s CC 663s Processing line... 663s GG 663s GG 663s Processing line... 663s Processing line... 663s Processing line... 663s CGTG 663s CGTG 663s Processing line... 663s CGTG 663s CGTG 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s GGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAG 663s GGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAG 663s Processing line... 663s AGGAGGG 663s AGGAGGG 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s AC 663s AC 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s AC 663s AC 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s Processing line... 663s AC 663s AC 663s Processing line... 663s GT 663s GT 663s Processing line... 663s GT 663s GT 663s --- Summary --- 663s Read 1 reference strings 663s Checked 131 alignments, 0 edits 663s --------------- 663s PASSED 663s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 663s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 663s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 663s Warning: skipping read '3' because length (1) <= # seed mismatches (1) 663s Warning: skipping read '3' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 663s Warning: skipping read '9' because length (1) <= # seed mismatches (1) 663s Warning: skipping read '9' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 663s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '14' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 663s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '29' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 663s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '31' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 663s Warning: skipping read '51' because length (1) <= # seed mismatches (1) 663s Warning: skipping read '51' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 663s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '75' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 663s 76 reads; of these: 663s 76 (100.00%) were unpaired; of these: 663s 62 (81.58%) aligned 0 times 663s 7 (9.21%) aligned exactly 1 time 663s 7 (9.21%) aligned >1 times 663s 18.42% overall alignment rate 663s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 663s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 663s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 663s /usr/bin/bowtie2 --cp-min 2 -a --cp-ival 1 --trim3 1 --ma 24.6490870919881 --score-min L,4.52728145840528,7.06411031049182 -N 1 -L29 --rdg 20.3726899822609,2.1357875701701 --mm --rfg 38.1751700993113,14.8540403114601 -q -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 663s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 663s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 663s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 663s Warning: skipping read '3' because length (1) <= # seed mismatches (1) 663s Warning: skipping read '3' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 663s Warning: skipping read '9' because length (1) <= # seed mismatches (1) 663s Warning: skipping read '9' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 663s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '14' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 663s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '29' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 663s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '31' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 663s Warning: skipping read '51' because length (1) <= # seed mismatches (1) 663s Warning: skipping read '51' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 663s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '75' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 663s 76 reads; of these: 663s 76 (100.00%) were unpaired; of these: 663s 62 (81.58%) aligned 0 times 663s 7 (9.21%) aligned exactly 1 time 663s 7 (9.21%) aligned >1 times 663s 18.42% overall alignment rate 663s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 663s Flattened IUPAC characters 663s Mutating sequence Sim.pm.1 663s Introducing 4 SNPs, 1/0 ref/read gaps, and 1 rearrangements 663s Finished SNPs 663s Finished ref gaps 663s Finished read gaps 663s Mutating sequence Sim.pm.2 663s Introducing 13 SNPs, 1/1 ref/read gaps, and 0 rearrangements 663s Finished SNPs 663s Finished ref gaps 663s Finished read gaps 663s Mutated reference genome to subject genome 663s SNPs introduced: 17 663s Reference gaps introduced: 2 663s Read gaps introduced: 1 663s Rearrangements introduced: 1 663s Created read sampler 663s Sampling 55 reads 663s *** Run 7 of 100 663s /usr/bin/bowtie2 --ma 1.09329398066271 --score-min L,1.36660920417019,3.62579420823255 -D 44 --gbar 7 --rdg 2.62376995618476 --mm --np 2 --cp-min 19 --nofw --trim3 3 --norc --cp-ival 3 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 663s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 663s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 663s parsing sequence Sim.pm.1... 663s parsing sequence Sim.pm.2... 663s Parsed 143 reference bases 663s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 663s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 663s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 663s Warning: skipping read '15' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 663s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 663s Warning: skipping read '21' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 663s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 663s Warning: skipping read '29' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 663s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 663s Warning: skipping read '43' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 663s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 663s Warning: skipping read '54' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 663s 55 reads; of these: 663s 55 (100.00%) were unpaired; of these: 663s 55 (100.00%) aligned 0 times 663s 0 (0.00%) aligned exactly 1 time 663s 0 (0.00%) aligned >1 times 663s 0.00% overall alignment rate 663s Read 50 alignments... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s --- Summary --- 663s Read 1 reference strings 663s Checked 0 alignments, 0 edits 663s --------------- 663s PASSED 663s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 663s /usr/bin/bowtie2 --ma 1.09329398066271 --score-min L,1.36660920417019,3.62579420823255 -D 44 --gbar 7 --rdg 2.62376995618476 --mm --np 2 --cp-min 19 --nofw --trim3 3 --norc --cp-ival 3 -f -p 3 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 663s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 663s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 663s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 663s Warning: skipping read '15' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 663s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 663s Warning: skipping read '21' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 663s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 663s Warning: skipping read '29' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 663s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 663s Warning: skipping read '43' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 663s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 663s Warning: skipping read '54' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 663s 55 reads; of these: 663s 55 (100.00%) were unpaired; of these: 663s 55 (100.00%) aligned 0 times 663s 0 (0.00%) aligned exactly 1 time 663s 0 (0.00%) aligned >1 times 663s 0.00% overall alignment rate 663s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 663s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 663s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 663s Flattened IUPAC characters 663s Mutating sequence Sim.pm.1 663s Introducing 15 SNPs, 1/6 ref/read gaps, and 0 rearrangements 663s Finished SNPs 663s Finished ref gaps 663s Finished read gaps 663s Mutating sequence Sim.pm.2 663s Introducing 6 SNPs, 2/0 ref/read gaps, and 0 rearrangements 663s Finished SNPs 663s Finished ref gaps 663s Finished read gaps 663s Mutated reference genome to subject genome 663s SNPs introduced: 21 663s Reference gaps introduced: 3 663s Read gaps introduced: 6 663s Rearrangements introduced: 0 663s Created read sampler 663s Sampling 113 reads 663s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 663s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 663s parsing sequence Sim.pm.1... 663s parsing sequence Sim.pm.2... 663s Parsed 143 reference bases 663s *** Run 8 of 100 663s /usr/bin/bowtie2 --local --rdg 33.258151060875 --cp-ival 1 --score-min L,9.92669717770501,8.71364612116475 --cp-min 5 --gbar 3 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 663s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 663s Warning: skipping mate #2 of read '41' because it was < 2 characters long 663s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 663s Warning: skipping mate #1 of read '48' because it was < 2 characters long 663s Read 50 alignments... 663s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 663s Warning: skipping mate #1 of read '96' because it was < 2 characters long 663s Read 100 alignments... 663s Read 150 alignments... 663s 113 reads; of these: 663s 113 (100.00%) were paired; of these: 663s 113 (100.00%) aligned concordantly 0 times 663s 0 (0.00%) aligned concordantly exactly 1 time 663s 0 (0.00%) aligned concordantly >1 times 663s ---- 663s 113 pairs aligned concordantly 0 times; of these: 663s 0 (0.00%) aligned discordantly 1 time 663s ---- 663s 113 pairs aligned 0 times concordantly or discordantly; of these: 663s 226 mates make up the pairs; of these: 663s 226 (100.00%) aligned 0 times 663s 0 (0.00%) aligned exactly 1 time 663s 0 (0.00%) aligned >1 times 663s 0.00% overall alignment rate 663s Read 200 alignments... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s *** Run 9 of 100 663s /usr/bin/bowtie2 -N 1 -L15 --trim3 8 --nofw --score-min L,3.47166668115727,7.75886523234823 --n-ceil 0.268433132822074,1.45630840178868 --cp-min 5 --np 1 -a --cp-ival 1 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s --- Summary --- 663s Read 1 reference strings 663s Checked 0 alignments, 0 edits 663s --------------- 663s PASSED 663s Flattened IUPAC characters 663s Mutating sequence Sim.pm.1 663s Introducing 18 SNPs, 1/2 ref/read gaps, and 2 rearrangements 663s Finished SNPs 663s Finished ref gaps 663s Finished read gaps 663s Mutating sequence Sim.pm.2 663s Introducing 2 SNPs, 1/0 ref/read gaps, and 2 rearrangements 663s Finished SNPs 663s Finished ref gaps 663s Finished read gaps 663s Mutated reference genome to subject genome 663s SNPs introduced: 20 663s Reference gaps introduced: 2 663s Read gaps introduced: 2 663s Rearrangements introduced: 4 663s Created read sampler 663s Sampling 66 reads 663s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 663s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 663s parsing sequence Sim.pm.1... 663s parsing sequence Sim.pm.2... 663s Parsed 143 reference bases 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 663s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '4' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 663s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '7' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 663s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '10' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 663s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (1) 663s Warning: skipping mate #2 of read '15' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 663s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '36' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 663s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '48' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 663s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '52' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 663s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (1) 663s Warning: skipping mate #2 of read '53' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 663s Warning: skipping read '56' because length (1) <= # seed mismatches (1) 663s Warning: skipping read '56' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 663s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '57' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 663s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '64' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 663s Read 50 alignments... 663s Read 100 alignments... 663s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 663s 66 reads; of these: 663s 50 (75.76%) were paired; of these: 663s 49 (98.00%) aligned concordantly 0 times 663s 1 (2.00%) aligned concordantly exactly 1 time 663s 0 (0.00%) aligned concordantly >1 times 663s ---- 663s 49 pairs aligned concordantly 0 times; of these: 663s 2 (4.08%) aligned discordantly 1 time 663s ---- 663s 47 pairs aligned 0 times concordantly or discordantly; of these: 663s 94 mates make up the pairs; of these: 663s 87 (92.55%) aligned 0 times 663s 4 (4.26%) aligned exactly 1 time 663s 3 (3.19%) aligned >1 times 663s 16 (24.24%) were unpaired; of these: 663s 15 (93.75%) aligned 0 times 663s 0 (0.00%) aligned exactly 1 time 663s 1 (6.25%) aligned >1 times 663s 12.07% overall alignment rate 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s AGG 663s AGG 663s Processing line... 663s AGG 663s AGG 663s Processing line... 663s AGG 663s AGG 663s Processing line... 663s AGG 663s AGG 663s Processing line... 663s AGG 663s AGG 663s Processing line... 663s AGG 663s AGG 663s Processing line... 663s AGG 663s AGG 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s CCGCGGCTCGGTCTGCGCCCAGCTTAG 663s CCGCGGCTCGGTCTGCGCCCAGCTTAG 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s CTGGC 663s CTGGC 663s Processing line... 663s GGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCG 663s GGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCG 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s TGGT 663s TGGT 663s Processing line... 663s TGGT 663s TGGT 663s Processing line... 663s TGGT 663s TGGT 663s Processing line... 663s TGGT 663s TGGT 663s Processing line... 663s TGGT 663s TGGT 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s CTGGCGGGAAGACCGCGGCTCGGTCT 663s CTGGCGGGAAGACCGCGGCTCGGTCT 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s GGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCC 663s GGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCC 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s CTTAGGCGGTCAGGAG 663s CTTAGGCGGTCAGGAG 663s Processing line... 663s GGGGGGACTGGCGG 663s GGGGGGACTGGCGG 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s ACTG 663s ACTG 663s Processing line... 663s GACCGCGGCTCGG 663s GACCGCGGCTCGG 663s Processing line... 663s Processing line... 663s /usr/bin/bowtie2 -N 1 -L15 --trim3 8 --nofw --score-min L,3.47166668115727,7.75886523234823 --n-ceil 0.268433132822074,1.45630840178868 --cp-min 5 --np 1 -a --cp-ival 1 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s AG 663s AG 663s Processing line... 663s AG 663s AG 663s Processing line... 663s AG 663s AG 663s Processing line... 663s AG 663s AG 663s Processing line... 663s AG 663s AG 663s Processing line... 663s AG 663s AG 663s Processing line... 663s AG 663s AG 663s Processing line... 663s AG 663s AG 663s Processing line... 663s AG 663s AG 663s Processing line... 663s AG 663s AG 663s Processing line... 663s AG 663s AG 663s Processing line... 663s AG 663s AG 663s Processing line... 663s AG 663s AG 663s Processing line... 663s CCGGGTGGTGTTGAGA 663s CCGGGTGGTGTTGAGA 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s CGC 663s CGC 663s Processing line... 663s CGC 663s CGC 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s Processing line... 663s --- Summary --- 663s Read 1 reference strings 663s Checked 37 alignments, 0 edits 663s --------------- 663s PASSED 663s ALSO checking that bowtie2 and bowtie2-align match up 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 663s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '4' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 663s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '7' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 663s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '10' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 663s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (1) 663s Warning: skipping mate #2 of read '15' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 663s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '36' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 663s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '48' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 663s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '52' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 663s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (1) 663s Warning: skipping mate #2 of read '53' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 663s Warning: skipping read '56' because length (1) <= # seed mismatches (1) 663s Warning: skipping read '56' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 663s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '57' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 663s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '64' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 663s 66 reads; of these: 663s 50 (75.76%) were paired; of these: 663s 49 (98.00%) aligned concordantly 0 times 663s 1 (2.00%) aligned concordantly exactly 1 time 663s 0 (0.00%) aligned concordantly >1 times 663s ---- 663s 49 pairs aligned concordantly 0 times; of these: 663s 2 (4.08%) aligned discordantly 1 time 663s ---- 663s 47 pairs aligned 0 times concordantly or discordantly; of these: 663s 94 mates make up the pairs; of these: 663s 87 (92.55%) aligned 0 times 663s 4 (4.26%) aligned exactly 1 time 663s 3 (3.19%) aligned >1 times 663s 16 (24.24%) were unpaired; of these: 663s 15 (93.75%) aligned 0 times 663s 0 (0.00%) aligned exactly 1 time 663s 1 (6.25%) aligned >1 times 663s 12.07% overall alignment rate 663s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 663s /usr/bin/bowtie2 -N 1 -L15 --trim3 8 --nofw --score-min L,3.47166668115727,7.75886523234823 --n-ceil 0.268433132822074,1.45630840178868 --cp-min 5 --np 1 -a --cp-ival 1 -q -p 4 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 663s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 663s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '4' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 663s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '7' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 663s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '10' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 663s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (1) 663s Warning: skipping mate #2 of read '15' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 663s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '36' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 663s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '48' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 663s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 663s Warning: skipping read '52' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 663s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (1) 663s Warning: skipping mate #2 of read '53' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 663s Warning: skipping read '56' because length (1) <= # seed mismatches (1) 663s Warning: skipping read '56' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 663s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '57' because it was < 2 characters long 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 663s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 663s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (1) 663s Warning: skipping mate #1 of read '64' because it was < 2 characters long 663s 66 reads; of these: 663s 50 (75.76%) were paired; of these: 663s 49 (98.00%) aligned concordantly 0 times 663s 1 (2.00%) aligned concordantly exactly 1 time 663s 0 (0.00%) aligned concordantly >1 times 663s ---- 663s 49 pairs aligned concordantly 0 times; of these: 663s 2 (4.08%) aligned discordantly 1 time 663s ---- 663s 47 pairs aligned 0 times concordantly or discordantly; of these: 663s 94 mates make up the pairs; of these: 663s 87 (92.55%) aligned 0 times 663s 4 (4.26%) aligned exactly 1 time 663s 3 (3.19%) aligned >1 times 663s 16 (24.24%) were unpaired; of these: 663s 15 (93.75%) aligned 0 times 663s 0 (0.00%) aligned exactly 1 time 663s 1 (6.25%) aligned >1 times 663s 12.07% overall alignment rate 663s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 663s Flattened IUPAC characters 663s Mutating sequence Sim.pm.2 663s Introducing 8 SNPs, 0/0 ref/read gaps, and 2 rearrangements 663s Finished SNPs 663s Finished ref gaps 663s Finished read gaps 663s Mutating sequence Sim.pm.1 663s Introducing 12 SNPs, 0/0 ref/read gaps, and 0 rearrangements 663s Finished SNPs 663s Finished ref gaps 663s Finished read gaps 663s Mutated reference genome to subject genome 663s SNPs introduced: 20 663s Reference gaps introduced: 0 663s Read gaps introduced: 0 663s Rearrangements introduced: 2 663s Created read sampler 663s Sampling 184 reads 663s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 663s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 663s parsing sequence Sim.pm.1... 663s parsing sequence Sim.pm.2... 663s Parsed 143 reference bases 663s *** Run 10 of 100 663s /usr/bin/bowtie2 --cp-min 3 --np 1 --rdg 42.1161090139622 --score-min L,3.60462662875339,9.99585865654423 --local --cp-ival 4 -a --trim3 7 --nofw -i C,1.29561095970074 --mp 8.93333110554756,6.11082446827557 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq 664s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 664s Read 50 alignments... 664s Warning: skipping read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 664s Read 100 alignments... 664s Warning: skipping read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_154_154_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_154_154_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_161_161_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_161_161_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_165_165_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_165_165_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_168_168_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_169_169_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_169_169_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_183_183_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_183_183_1/1' because it was < 2 characters long 664s 184 reads; of these: 664s 184 (100.00%) were unpaired; of these: 664s 184 (100.00%) aligned 0 times 664s 0 (0.00%) aligned exactly 1 time 664s 0 (0.00%) aligned >1 times 664s 0.00% overall alignment rate 664s Read 150 alignments... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s /usr/bin/bowtie2 --cp-min 3 --np 1 --rdg 42.1161090139622 --score-min L,3.60462662875339,9.99585865654423 --local --cp-ival 4 -a --trim3 7 --nofw -i C,1.29561095970074 --mp 8.93333110554756,6.11082446827557 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s --- Summary --- 664s Read 1 reference strings 664s Checked 0 alignments, 0 edits 664s --------------- 664s PASSED 664s ALSO checking that bowtie2 and bowtie2-align match up 664s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_154_154_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_154_154_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_161_161_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_161_161_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_165_165_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_165_165_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_168_168_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_169_169_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_169_169_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_183_183_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_183_183_1/1' because it was < 2 characters long 664s 184 reads; of these: 664s 184 (100.00%) were unpaired; of these: 664s 184 (100.00%) aligned 0 times 664s 0 (0.00%) aligned exactly 1 time 664s 0 (0.00%) aligned >1 times 664s 0.00% overall alignment rate 664s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 664s /usr/bin/bowtie2 --cp-min 3 --np 1 --rdg 42.1161090139622 --score-min L,3.60462662875339,9.99585865654423 --local --cp-ival 4 -a --trim3 7 --nofw -i C,1.29561095970074 --mp 8.93333110554756,6.11082446827557 --qseq -p 3 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 664s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 664s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_154_154_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_154_154_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_161_161_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_161_161_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_165_165_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_165_165_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_168_168_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_169_169_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_169_169_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_183_183_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_183_183_1/1' because it was < 2 characters long 664s 184 reads; of these: 664s 184 (100.00%) were unpaired; of these: 664s 184 (100.00%) aligned 0 times 664s 0 (0.00%) aligned exactly 1 time 664s 0 (0.00%) aligned >1 times 664s 0.00% overall alignment rate 664s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 664s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 664s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 664s /usr/bin/bowtie2 --cp-min 3 --np 1 --rdg 42.1161090139622 --score-min L,3.60462662875339,9.99585865654423 --local --cp-ival 4 -a --trim3 7 --nofw -i C,1.29561095970074 --mp 8.93333110554756,6.11082446827557 --qseq -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 664s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 664s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_154_154_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_154_154_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_161_161_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_161_161_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_165_165_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_165_165_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_168_168_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_169_169_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_169_169_1/1' because it was < 2 characters long 664s Warning: skipping read 'R_1_1_1_183_183_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_183_183_1/1' because it was < 2 characters long 664s 184 reads; of these: 664s 184 (100.00%) were unpaired; of these: 664s 184 (100.00%) aligned 0 times 664s 0 (0.00%) aligned exactly 1 time 664s 0 (0.00%) aligned >1 times 664s 0.00% overall alignment rate 664s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 664s Flattened IUPAC characters 664s Mutating sequence Sim.pm.1 664s Introducing 2 SNPs, 3/0 ref/read gaps, and 2 rearrangements 664s Finished SNPs 664s Finished ref gaps 664s Finished read gaps 664s Mutating sequence Sim.pm.2 664s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 664s Finished SNPs 664s Finished ref gaps 664s Finished read gaps 664s Mutated reference genome to subject genome 664s SNPs introduced: 12 664s Reference gaps introduced: 3 664s Read gaps introduced: 0 664s Rearrangements introduced: 2 664s Created read sampler 664s Sampling 63 reads 664s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 664s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 664s parsing sequence Sim.pm.1... 664s *** Run 11 of 100 664s /usr/bin/bowtie2 --rdg 41.1560505410956,7.77097049706266 --score-min L,8.42272537990085,6.14204030720211 -k 2 -D 27 --np 7 --cp-min 4 --rfg 22.7135547691268 --trim3 6 --mp 6.53996706888881,1.18999086746444 --local --cp-ival 2 -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta 664s parsing sequence Sim.pm.2... 664s Parsed 143 reference bases 664s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 664s Warning: skipping mate #1 of read '6' because it was < 2 characters long 664s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 664s Warning: skipping mate #1 of read '13' because it was < 2 characters long 664s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 664s Warning: skipping mate #1 of read '28' because it was < 2 characters long 664s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 664s Warning: skipping mate #1 of read '29' because it was < 2 characters long 664s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 664s Warning: skipping mate #1 of read '37' because it was < 2 characters long 664s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 664s Warning: skipping read '46' because it was < 2 characters long 664s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 664s Warning: skipping mate #2 of read '63' because it was < 2 characters long 664s 63 reads; of these: 664s 57 (90.48%) were paired; of these: 664s 57 (100.00%) aligned concordantly 0 times 664s 0 (0.00%) aligned concordantly exactly 1 time 664s 0 (0.00%) aligned concordantly >1 times 664s ---- 664s 57 pairs aligned concordantly 0 times; of these: 664s 0 (0.00%) aligned discordantly 1 time 664s ---- 664s 57 pairs aligned 0 times concordantly or discordantly; of these: 664s 114 mates make up the pairs; of these: 664s 114 (100.00%) aligned 0 times 664s 0 (0.00%) aligned exactly 1 time 664s 0 (0.00%) aligned >1 times 664s 6 (9.52%) were unpaired; of these: 664s 6 (100.00%) aligned 0 times 664s 0 (0.00%) aligned exactly 1 time 664s 0 (0.00%) aligned >1 times 664s 0.00% overall alignment rate 664s Read 50 alignments... 664s Read 100 alignments... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s --- Summary --- 664s Read 1 reference strings 664s Checked 0 alignments, 0 edits 664s --------------- 664s PASSED 664s Flattened IUPAC characters 664s Mutating sequence Sim.pm.1 664s Introducing 17 SNPs, 1/2 ref/read gaps, and 1 rearrangements 664s Finished SNPs 664s Finished ref gaps 664s Finished read gaps 664s Mutating sequence Sim.pm.2 664s Introducing 17 SNPs, 0/1 ref/read gaps, and 0 rearrangements 664s Finished SNPs 664s Finished ref gaps 664s Finished read gaps 664s Mutated reference genome to subject genome 664s SNPs introduced: 34 664s Reference gaps introduced: 1 664s Read gaps introduced: 3 664s Rearrangements introduced: 1 664s Created read sampler 664s Sampling 28 reads 664s *** Run 12 of 100 664s /usr/bin/bowtie2 --cp-min 3 -M 4 --trim5 9 --cp-ival 1 --trim3 1 --score-min L,1.12665662205117,9.38299411048857 -D 9 --rfg 4.04873116414163,19.8918027760476 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq 664s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 664s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 664s parsing sequence Sim.pm.1... 664s parsing sequence Sim.pm.2... 664s Parsed 143 reference bases 664s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 664s 28 reads; of these: 664s 28 (100.00%) were unpaired; of these: 664s 24 (85.71%) aligned 0 times 664s 4 (14.29%) aligned exactly 1 time 664s 0 (0.00%) aligned >1 times 664s 14.29% overall alignment rate 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s TTGAG 664s TTGAG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s ACTGGCGGGAAGACC 664s ACTGGCGGGAAGACC 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s CGGTCTG 664s CGGTCTG 664s Processing line... 664s GGTGGTGTTGAGAGGGT 664s GGTGGTGTTGAGAGGGT 664s Processing line... 664s Processing line... 664s Processing line... 664s /usr/bin/bowtie2 --cp-min 3 -M 4 --trim5 9 --cp-ival 1 --trim3 1 --score-min L,1.12665662205117,9.38299411048857 -D 9 --rfg 4.04873116414163,19.8918027760476 --qseq -p 2 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s --- Summary --- 664s Read 1 reference strings 664s Checked 4 alignments, 0 edits 664s --------------- 664s PASSED 664s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 664s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 664s 28 reads; of these: 664s 28 (100.00%) were unpaired; of these: 664s 24 (85.71%) aligned 0 times 664s 4 (14.29%) aligned exactly 1 time 664s 0 (0.00%) aligned >1 times 664s 14.29% overall alignment rate 664s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 664s Flattened IUPAC characters 664s Mutating sequence Sim.pm.2 664s Introducing 14 SNPs, 1/1 ref/read gaps, and 2 rearrangements 664s Finished SNPs 664s Finished ref gaps 664s Finished read gaps 664s Mutating sequence Sim.pm.1 664s Introducing 3 SNPs, 1/2 ref/read gaps, and 1 rearrangements 664s Finished SNPs 664s Finished ref gaps 664s Finished read gaps 664s Mutated reference genome to subject genome 664s SNPs introduced: 17 664s Reference gaps introduced: 2 664s Read gaps introduced: 3 664s Rearrangements introduced: 3 664s Created read sampler 664s Sampling 117 reads 664s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 664s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 664s parsing sequence Sim.pm.1... 664s *** Run 13 of 100 664s /usr/bin/bowtie2 --np 3 --cp-min 2 --trim5 6 --cp-ival 1 --score-min L,7.47319806703452,8.22923546586419 --nofw -R 3 --mp 9.02642752893565,8.5135420847922 --rdg 45.4774264053354 --rfg 2.23927294618366 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 664s parsing sequence Sim.pm.2... 664s Parsed 143 reference bases 664s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 664s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '6' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 664s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '11' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 664s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '12' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 664s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '17' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 664s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 664s Warning: skipping read '24' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 664s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '36' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 664s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '40' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 664s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '47' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 664s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '50' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 664s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '54' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 664s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '56' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 664s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '63' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 664s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '67' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 664s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 664s Warning: skipping read '71' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 664s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '73' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 664s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '74' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 664s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '82' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 664s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '84' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 664s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '85' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 664s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 664s Warning: skipping read '86' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 664s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '90' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 664s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '107' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 664s 117 reads; of these: 664s 117 (100.00%) were unpaired; of these: 664s 102 (87.18%) aligned 0 times 664s 8 (6.84%) aligned exactly 1 time 664s 7 (5.98%) aligned >1 times 664s 12.82% overall alignment rate 664s Read 50 alignments... 664s Read 100 alignments... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s CGGGTGG 664s CGGGTGG 664s Processing line... 664s GGCGGG 664s GGCGGG 664s Processing line... 664s Processing line... 664s GACCGC 664s GACCGC 664s Processing line... 664s Processing line... 664s Processing line... 664s /usr/bin/bowtie2 --np 3 --cp-min 2 --trim5 6 --cp-ival 1 --score-min L,7.47319806703452,8.22923546586419 --nofw -R 3 --mp 9.02642752893565,8.5135420847922 --rdg 45.4774264053354 --rfg 2.23927294618366 -f -p 4 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s CTGGCGGGA 664s CTGGCGGGA 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s CTCGGTCTGCGCCCAGCTTAG 664s CTCGGTCTGCGCCCAGCTTAG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s TCCG 664s TCCG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s GTGGTGTTG 664s GTGGTGTTG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s TCCG 664s TCCG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s GTGGTGTTGAGA 664s GTGGTGTTGAGA 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s CTGG 664s CTGG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s CGCGGCTC 664s CGCGGCTC 664s Processing line... 664s Processing line... 664s Processing line... 664s GGCT 664s GGCT 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s CAG 664s CAG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s CGGGTGGTGTTGAGAGGGTG 664s CGGGTGGTGTTGAGAGGGTG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s CA 664s CA 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s --- Summary --- 664s Read 1 reference strings 664s Checked 15 alignments, 0 edits 664s --------------- 664s PASSED 664s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 664s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 664s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '6' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 664s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '11' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 664s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '12' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 664s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '17' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 664s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 664s Warning: skipping read '24' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 664s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '36' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 664s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '40' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 664s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '47' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 664s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '50' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 664s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '54' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 664s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '56' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 664s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '63' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 664s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '67' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 664s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 664s Warning: skipping read '71' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 664s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '73' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 664s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '74' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 664s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '82' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 664s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '84' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 664s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '85' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 664s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 664s Warning: skipping read '86' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 664s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '90' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 664s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 664s Warning: skipping read '107' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 664s 117 reads; of these: 664s 117 (100.00%) were unpaired; of these: 664s 102 (87.18%) aligned 0 times 664s 8 (6.84%) aligned exactly 1 time 664s 7 (5.98%) aligned >1 times 664s 12.82% overall alignment rate 664s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 664s Flattened IUPAC characters 664s Mutating sequence Sim.pm.2 664s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 664s Finished SNPs 664s Finished ref gaps 664s Finished read gaps 664s Mutating sequence Sim.pm.1 664s Introducing 12 SNPs, 0/0 ref/read gaps, and 2 rearrangements 664s Finished SNPs 664s Finished ref gaps 664s Finished read gaps 664s Mutated reference genome to subject genome 664s SNPs introduced: 17 664s Reference gaps introduced: 0 664s Read gaps introduced: 1 664s Rearrangements introduced: 2 664s Created read sampler 664s Sampling 121 reads 664s *** Run 14 of 100 664s /usr/bin/bowtie2 --mm --score-min L,6.74890647812609,8.90876191493346 --trim3 7 --ma 3.59443945881322 -D 39 --mp 8.25549565102772,6.45502529464529 --cp-ival 2 --cp-min 3 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq 664s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 664s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 664s parsing sequence Sim.pm.1... 664s parsing sequence Sim.pm.2... 664s Parsed 143 reference bases 664s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (1) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 664s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 664s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 664s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 664s Read 50 alignments... 664s 121 Read 100 alignments... 664s reads; of these: 664s 121 (100.00%) were unpaired; of these: 664s 104 (85.95%) aligned 0 times 664s 8 (6.61%) aligned exactly 1 time 664s 9 (7.44%) aligned >1 times 664s 14.05% overall alignment rate 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s GTGT 664s GTGT 664s Processing line... 664s Processing line... 664s TC 664s TC 664s Processing line... 664s GTGT 664s GTGT 664s Processing line... 664s Processing line... 664s Processing line... 664s GGTCAGG 664s GGTCAGG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s TGGTGGTAGGGGGGGACTG 664s TGGTGGTAGGGGGGGACTG 664s Processing line... 664s Processing line... 664s Processing line... 664s GCGGTC 664s GCGGTC 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s GG 664s GG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s GTTGAGAG 664s GTTGAGAG 664s Processing line... 664s CTGGCGG 664s CTGGCGG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s ACCGCGGC 664s ACCGCGGC 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s GGG 664s GGG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s TG 664s TG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s GGGGGACTGG 664s GGGGGACTGG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s GGCG 664s GGCG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s GAGAGG 664s GAGAGG 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s GGTGGTGTTGAGAGGGTGACA 664s GGTGGTGTTGAGAGGGTGACA 664s Processing line... 664s Processing line... 664s Processing line... 664s GT 664s GT 664s Processing line... 664s Processing line... 664s Processing line... 664s Processing line... 664s --- Summary --- 664s Read 1 reference strings 664s Checked 17 alignments, 0 edits 664s --------------- 664s PASSED 664s ALSO checking that bowtie2 and bowtie2-align match up 664s /usr/bin/bowtie2 --mm --score-min L,6.74890647812609,8.90876191493346 --trim3 7 --ma 3.59443945881322 -D 39 --mp 8.25549565102772,6.45502529464529 --cp-ival 2 --cp-min 3 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 665s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 665s 121 reads; of these: 665s 121 (100.00%) were unpaired; of these: 665s 104 (85.95%) aligned 0 times 665s 8 (6.61%) aligned exactly 1 time 665s 9 (7.44%) aligned >1 times 665s 14.05% overall alignment rate 665s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 665s Flattened IUPAC characters 665s Mutating sequence Sim.pm.1 665s Introducing 18 SNPs, 2/0 ref/read gaps, and 0 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutating sequence Sim.pm.2 665s Introducing 5 SNPs, 1/1 ref/read gaps, and 0 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutated reference genome to subject genome 665s SNPs introduced: 23 665s Reference gaps introduced: 3 665s Read gaps introduced: 1 665s Rearrangements introduced: 0 665s Created read sampler 665s Sampling 9 reads 665s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 665s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 665s parsing sequence Sim.pm.1... 665s parsing sequence Sim.pm.2... 665s Parsed 143 reference bases 665s *** Run 15 of 100 665s /usr/bin/bowtie2 --cp-min 9 -a --cp-ival 1 --local -D 19 --trim3 2 --score-min L,6.3384796286797,5.59415405825856 --rdg 32.1263244942471 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 665s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '5' because it was < 2 characters long 665s 9 reads; of these: 665s 9 (100.00%) were unpaired; of these: 665s 9 (100.00%) aligned 0 times 665s 0 (0.00%) aligned exactly 1 time 665s 0 (0.00%) aligned >1 times 665s 0.00% overall alignment rate 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s --- Summary --- 665s Read 1 reference strings 665s Checked 0 alignments, 0 edits 665s --------------- 665s PASSED 665s Flattened IUPAC characters 665s Mutating sequence Sim.pm.2 665s Introducing 7 SNPs, 2/0 ref/read gaps, and 0 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutating sequence Sim.pm.1 665s Introducing 11 SNPs, 0/0 ref/read gaps, and 1 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutated reference genome to subject genome 665s SNPs introduced: 18 665s Reference gaps introduced: 2 665s Read gaps introduced: 0 665s Rearrangements introduced: 1 665s Created read sampler 665s Sampling 126 reads 665s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 665s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 665s parsing sequence Sim.pm.1... 665s parsing sequence Sim.pm.2... 665s Parsed 143 reference bases 665s *** Run 16 of 100 665s /usr/bin/bowtie2 --rdg 39.6631997755598,14.9891344951822 --mm --score-min L,7.20383474339077,3.66499332409558 -D 33 --np 3 --cp-min 2 --rfg 12.1953624806394,13.8621183211357 --nofw --mp 6.95874257920921,4.74980817629662 --cp-ival 1 --trim5 2 -q -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq 665s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 665s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '3' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 665s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '4' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 665s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 665s Warning: skipping read '7' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 665s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '11' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 665s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 665s Warning: skipping read '14' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 665s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 665s Warning: skipping read '39' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 665s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 665s Warning: skipping read '95' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 665s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '108' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 665s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '110' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 665s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '124' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 665s 126 reads; of these: 665s 126 (100.00%) were unpaired; of these: 665s 114 (90.48%) aligned 0 times 665s 6 (4.76%) aligned exactly 1 time 665s 6 (4.76%) aligned >1 times 665s 9.52% overall alignment rate 665s Read 50 alignments... 665s Read 100 alignments... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TCAGGAGGGAGC 665s TCAGGAGGGAGC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGTGGTAGGGGGGGACTGGCGG 665s GGTGGTAGGGGGGGACTGGCGG 665s Processing line... 665s Processing line... 665s GTGGTGTTGAGAGGGTGACAGAGG 665s GTGGTGTTGAGAGGGTGACAGAGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CAGC 665s CAGC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GC 665s GC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CGTGG 665s CGTGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GTGGTG 665s GTGGTG 665s Processing line... 665s TT 665s TT 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CGTGG 665s CGTGG 665s Processing line... 665s CAGGAGGGAGCTGG 665s CAGGAGGGAGCTGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CGG 665s CGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s ACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGC 665s ACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s --- Summary --- 665s Read 1 reference strings 665s Checked 12 alignments, 0 edits 665s --------------- 665s PASSED 665s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 665s /usr/bin/bowtie2 --rdg 39.6631997755598,14.9891344951822 --mm --score-min L,7.20383474339077,3.66499332409558 -D 33 --np 3 --cp-min 2 --rfg 12.1953624806394,13.8621183211357 --nofw --mp 6.95874257920921,4.74980817629662 --cp-ival 1 --trim5 2 -q -p 4 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 665s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 665s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '3' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 665s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '4' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 665s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 665s Warning: skipping read '7' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 665s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '11' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 665s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 665s Warning: skipping read '14' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 665s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 665s Warning: skipping read '39' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 665s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 665s Warning: skipping read '95' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 665s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '108' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 665s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '110' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 665s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '124' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 665s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 665s 126 reads; of these: 665s 126 (100.00%) were unpaired; of these: 665s 114 (90.48%) aligned 0 times 665s 6 (4.76%) aligned exactly 1 time 665s 6 (4.76%) aligned >1 times 665s 9.52% overall alignment rate 665s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 665s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 665s Flattened IUPAC characters 665s Mutating sequence Sim.pm.1 665s Introducing 7 SNPs, 2/1 ref/read gaps, and 0 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutating sequence Sim.pm.2 665s Introducing 9 SNPs, 0/2 ref/read gaps, and 0 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutated reference genome to subject genome 665s SNPs introduced: 16 665s Reference gaps introduced: 2 665s Read gaps introduced: 3 665s Rearrangements introduced: 0 665s Created read sampler 665s Sampling 188 reads 665s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 665s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 665s parsing sequence Sim.pm.1... 665s parsing sequence Sim.pm.2... 665s Parsed 143 reference bases 665s *** Run 17 of 100 665s /usr/bin/bowtie2 --score-min L,5.06572864464807,2.7245930491902 --trim3 2 --ma 24.4652818723344 -D 21 --rfg 47.963636549613 -M 4 --cp-min 10 --np 2 --cp-ival 1 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq 665s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 665s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_135_135_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_148_148_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_149_149_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_149_149_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_151_151_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_153_153_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_154_154_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_155_155_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_156_156_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_157_157_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_158_158_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_159_159_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_160_160_1/1; setting to 0 instead 665s Read 50 alignments... 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_161_161_1/1; setting to 0 instead 665s Read 100 alignments... 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_162_162_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_163_163_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_164_164_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_165_165_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_166_166_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_167_167_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_168_168_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_169_169_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_170_170_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_171_171_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_172_172_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_173_173_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_174_174_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_175_175_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_175_175_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_175_175_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_176_176_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_177_177_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_178_178_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_179_179_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_180_180_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_181_181_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_182_182_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_183_183_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_184_184_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_184_184_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_184_184_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_185_185_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_186_186_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_186_186_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_186_186_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_187_187_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_188_188_1/1; setting to 0 instead 665s 188 reads; of these: 665s 188 (100.00%) were unpaired; of these: 665s 155 (82.45%) aligned 0 times 665s 20 (10.64%) aligned exactly 1 time 665s 13 (6.91%) aligned >1 times 665s 17.55% overall alignment rate 665s Read 150 alignments... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGGG 665s GGGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s AGAGGGTGACAGAGGCGTG 665s AGAGGGTGACAGAGGCGTG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TCTGCGCCCAGCTTAGGCGGTCAG 665s TCTGCGCCCAGCTTAGGCGGTCAG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s AGAGG 665s AGAGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GG 665s GG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGTCAGGAGGGAGC 665s GGTCAGGAGGGAGC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGGGGGGACTG 665s GGGGGGGACTG 665s Processing line... 665s GTTGAGAGGGTG 665s GTTGAGAGGGTG 665s Processing line... 665s Processing line... 665s Processing line... 665s CAGAGG 665s CAGAGG 665s Processing line... 665s Processing line... 665s Processing line... 665s AAGACCGCG 665s AAGACCGCG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GTCAGGAGGGAGC 665s GTCAGGAGGGAGC 665s Processing line... 665s Processing line... 665s Processing line... 665s TCTGCGCC 665s TCTGCGCC 665s Processing line... 665s Processing line... 665s Processing line... 665s GTCTGCGCCCAGCTTA 665s GTCTGCGCCCAGCTTA 665s Processing line... 665s Processing line... 665s GGGGACTGGCGGGAAGACCGCGGCTCGGTCTGC 665s GGGGACTGGCGGGAAGACCGCGGCTCGGTCTGC 665s Processing line... 665s GGT 665s GGT 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGGGACTGGCGGGAAGACCGCGGCTC 665s GGGGACTGGCGGGAAGACCGCGGCTC 665s Processing line... 665s TGCGCCCAGC 665s TGCGCCCAGC 665s Processing line... 665s AG 665s AG 665s Processing line... 665s Processing line... 665s Processing line... 665s CCGCGGCTCGGTCT 665s CCGCGGCTCGGTCT 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GCGG 665s GCGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TT 665s TT 665s Processing line... 665s Processing line... 665s Processing line... 665s GGTGACAGA 665s GGTGACAGA 665s Processing line... 665s CTGCG 665s CTGCG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGT 665s GGT 665s Processing line... 665s Processing line... 665s Processing line... 665s GGT 665s GGT 665s Processing line... 665s TCTG 665s TCTG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s AGCTTAGGCG 665s AGCTTAGGCG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s AGGG 665s AGGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CGGGTGGTG 665s CGGGTGGTG 665s Processing line... 665s GGTGGTAGGGGGGGACTGGCGGGAAGACCG 665s GGTGGTAGGGGGGGACTGGCGGGAAGACCG 665s Processing line... 665s Processing line... 665s GGGAC 665s GGGAC 665s Processing line... 665s TGGT 665s TGGT 665s Processing line... 665s GGGGACTGGCGGGAAGACCGCGGCTC 665s GGGGACTGGCGGGAAGACCGCGGCTC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s --- Summary --- 665s Read 1 reference strings 665s Checked 33 alignments, 0 edits 665s --------------- 665s PASSED 665s Flattened IUPAC characters 665s Mutating sequence Sim.pm.1 665s Introducing 17 SNPs, 1/1 ref/read gaps, and 0 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutating sequence Sim.pm.2 665s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutated reference genome to subject genome 665s SNPs introduced: 25 665s Reference gaps introduced: 1 665s Read gaps introduced: 2 665s Rearrangements introduced: 0 665s Created read sampler 665s Sampling 128 reads 665s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 665s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 665s parsing sequence Sim.pm.1... 665s parsing sequence Sim.pm.2... 665s Parsed 143 reference bases 665s *** Run 18 of 100 665s /usr/bin/bowtie2 --rdg 11.0352314719906,11.5621594850829 --gbar 7 -i L,0.131943015016223 --score-min L,7.65447925246821,2.9559581867682 --nofw --trim3 1 --cp-ival 2 --cp-min 2 --np 1 -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 665s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '14' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 665s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '25' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 665s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '28' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 665s Read 50 alignments... 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 665s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '82' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 665s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '101' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 665s Read 100 alignments... 665s 128 reads; of these: 665s 126 (98.44%) were paired; of these: 665s 124 (98.41%) aligned concordantly 0 times 665s 0 (0.00%) aligned concordantly exactly 1 time 665s 2 (1.59%) aligned concordantly >1 times 665s ---- 665s 124 pairs aligned concordantly 0 times; of these: 665s 1 (0.81%) aligned discordantly 1 time 665s ---- 665s 123 pairs aligned 0 times concordantly or discordantly; of these: 665s 246 mates make up the pairs; of these: 665s 223 (90.65%) aligned 0 times 665s 8 (3.25%) aligned exactly 1 time 665s 15 (6.10%) aligned >1 times 665s 2 (1.56%) were unpaired; of these: 665s 2 (100.00%) aligned 0 times 665s 0 (0.00%) aligned exactly 1 time 665s 0 (0.00%) aligned >1 times 665s 11.42% overall alignment rate 665s Read 150 alignments... 665s Read 200 alignments... 665s Read 250 alignments... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GAGGCGTGG 665s GAGGCGTGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TG 665s TG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s AGGGGGGGACTGGC 665s AGGGGGGGACTGGC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s AC 665s AC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GAGG 665s GAGG 665s Processing line... 665s Processing line... 665s CGGGTGGTGTTGAGAGGGTGAC 665s CGGGTGGTGTTGAGAGGGTGAC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GG 665s GG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CGGTCTGCGC 665s CGGTCTGCGC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CGT 665s CGT 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s AG 665s AG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CAGCTTAGGCGGTCA 665s CAGCTTAGGCGGTCA 665s Processing line... 665s Processing line... 665s CA 665s CA 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CCGGGTGGTGTTGAGAGGGTGAC 665s CCGGGTGGTGTTGAGAGGGTGAC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GTGT 665s GTGT 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CGTGG 665s CGTGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TGGTG 665s TGGTG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s AG 665s AG 665s Processing line... 665s Processing line... 665s CAGC 665s CAGC 665s Processing line... 665s CG 665s CG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GG 665s GG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGGGAC 665s GGGGAC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGTGGTAGGGGGGGA 665s GGTGGTAGGGGGGGA 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TGT 665s TGT 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGAAGACCGCGGCTCGGTCTGCGCCCAG 665s GGAAGACCGCGGCTCGGTCTGCGCCCAG 665s Processing line... 665s AGGA 665s AGGA 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TGGTGG 665s TGGTGG 665s Processing line... 665s Processing line... 665s TGGTGTTGAG 665s TGGTGTTGAG 665s Processing line... 665s GA 665s GA 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGTAGGGGGGGAC 665s GGTAGGGGGGGAC 665s Processing line... 665s --- Summary --- 665s Read 1 reference strings 665s Checked 29 alignments, 0 edits 665s --------------- 665s PASSED 665s Flattened IUPAC characters 665s Mutating sequence Sim.pm.2 665s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutating sequence Sim.pm.1 665s Introducing 1 SNPs, 1/1 ref/read gaps, and 0 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutated reference genome to subject genome 665s SNPs introduced: 2 665s Reference gaps introduced: 1 665s Read gaps introduced: 2 665s Rearrangements introduced: 1 665s Created read sampler 665s Sampling 61 reads 665s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 665s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 665s parsing sequence Sim.pm.1... 665s parsing sequence Sim.pm.2... 665s Parsed 143 reference bases 665s *** Run 19 of 100 665s /usr/bin/bowtie2 --cp-ival 1 -a --cp-min 3 --score-min L,3.80254738042901,4.65822244852265 -N 0 -L29 --mp 7.95020623168327,7.8542240404566 -R 1 -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 665s Warning: skipping mate #2 of read '1' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #2 of read '1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 665s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '19' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 665s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '20' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 665s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #2 of read '35' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 665s Read 50 alignments... 665s Read 100 alignments... 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 665s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #2 of read '55' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 665s 61 reads; of these: 665s 61 (100.00%) were paired; of these: 665s 60 (98.36%) aligned concordantly 0 times 665s 0 (0.00%) aligned concordantly exactly 1 time 665s 1 (1.64%) aligned concordantly >1 times 665s ---- 665s 60 pairs aligned concordantly 0 times; of these: 665s 3 (5.00%) aligned discordantly 1 time 665s ---- 665s 57 pairs aligned 0 times concordantly or discordantly; of these: 665s 114 mates make up the pairs; of these: 665s 96 (84.21%) aligned 0 times 665s 11 (9.65%) aligned exactly 1 time 665s 7 (6.14%) aligned >1 times 665s 21.31% overall alignment rate 665s Read 150 alignments... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGT 665s GGT 665s Processing line... 665s CGCGGCTCGGTCTGC 665s CGCGGCTCGGTCTGC 665s Processing line... 665s GGT 665s GGT 665s Processing line... 665s CGCGGCTCGGTCTGC 665s CGCGGCTCGGTCTGC 665s Processing line... 665s GGT 665s GGT 665s Processing line... 665s CGCGGCTCGGTCTGC 665s CGCGGCTCGGTCTGC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s AA 665s AA 665s Processing line... 665s TT 665s TT 665s Processing line... 665s TT 665s TT 665s Processing line... 665s TT 665s TT 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TG 665s TG 665s Processing line... 665s CA 665s CA 665s Processing line... 665s CA 665s CA 665s Processing line... 665s TG 665s TG 665s Processing line... 665s TG 665s TG 665s Processing line... 665s TG 665s TG 665s Processing line... 665s TG 665s TG 665s Processing line... 665s TG 665s TG 665s Processing line... 665s TG 665s TG 665s Processing line... 665s TG 665s TG 665s Processing line... 665s TG 665s TG 665s Processing line... 665s CA 665s CA 665s Processing line... 665s TG 665s TG 665s Processing line... 665s TG 665s TG 665s Processing line... 665s TG 665s TG 665s Processing line... 665s TG 665s TG 665s Processing line... 665s TG 665s TG 665s Processing line... 665s TG 665s TG 665s Processing line... 665s Processing line... 665s GGG 665s GGG 665s Processing line... 665s GGG 665s GGG 665s Processing line... 665s GGG 665s GGG 665s Processing line... 665s GGG 665s GGG 665s Processing line... 665s GGG 665s GGG 665s Processing line... 665s GGG 665s GGG 665s Processing line... 665s CCC 665s CCC 665s Processing line... 665s GGG 665s GGG 665s Processing line... 665s GGG 665s GGG 665s Processing line... 665s GGG 665s GGG 665s Processing line... 665s GGG 665s GGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s ACTGGCGGGAAGACCGCGGCTCGGTCTGCGCC 665s ACTGGCGGGAAGACCGCGGCTCGGTCTGCGCC 665s Processing line... 665s AGGGA 665s AGGGA 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CCGCGGCTCGGTCTGCGCCCAGCTTAGGCGG 665s CCGCGGCTCGGTCTGCGCCCAGCTTAGGCGG 665s Processing line... 665s GACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAG 665s GACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAG 665s Processing line... 665s GAGAGGGTGACAGAGGCG 665s GAGAGGGTGACAGAGGCG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGTGTTGAGAGGGTGA 665s GGTGTTGAGAGGGTGA 665s Processing line... 665s Processing line... 665s AGGC 665s AGGC 665s Processing line... 665s AGGC 665s AGGC 665s Processing line... 665s AGGC 665s AGGC 665s Processing line... 665s Processing line... 665s AGAGGC 665s AGAGGC 665s Processing line... 665s AGAGGC 665s AGAGGC 665s Processing line... 665s Processing line... 665s GGTGGTGTTGAGAGGGTGACAGAG 665s GGTGGTGTTGAGAGGGTGACAGAG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CCCAGCTTA 665s CCCAGCTTA 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TGGTGTTGAGAGGGTGAC 665s TGGTGTTGAGAGGGTGAC 665s Processing line... 665s Processing line... 665s GACCGCGGCTCGGTCTGCGCCCA 665s GACCGCGGCTCGGTCTGCGCCCA 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGGGGGGACTGGCGGGAAGACCGCGGCTCGG 665s GGGGGGGACTGGCGGGAAGACCGCGGCTCGG 665s Processing line... 665s GGGGGGACT 665s GGGGGGACT 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s AGGGG 665s AGGGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GACAGAGGCGTG 665s GACAGAGGCGTG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GAGAG 665s GAGAG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GA 665s GA 665s Processing line... 665s GA 665s GA 665s Processing line... 665s GA 665s GA 665s Processing line... 665s TC 665s TC 665s Processing line... 665s GA 665s GA 665s Processing line... 665s GA 665s GA 665s Processing line... 665s GA 665s GA 665s Processing line... 665s TC 665s TC 665s Processing line... 665s GA 665s GA 665s Processing line... 665s GA 665s GA 665s Processing line... 665s GA 665s GA 665s Processing line... 665s TC 665s TC 665s Processing line... 665s GA 665s GA 665s Processing line... 665s GA 665s GA 665s Processing line... 665s TC 665s TC 665s Processing line... 665s TC 665s TC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TGG 665s TGG 665s Processing line... 665s TGG 665s TGG 665s Processing line... 665s TGG 665s TGG 665s Processing line... 665s TGG 665s TGG 665s Processing line... 665s CCA 665s CCA 665s Processing line... 665s TGG 665s TGG 665s Processing line... 665s TGG 665s TGG 665s Processing line... 665s TGG 665s TGG 665s Processing line... 665s TGG 665s TGG 665s Processing line... 665s TGG 665s TGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CGCCCAGCTTAGGCGGTCAGGAGGGAGCTG 665s CGCCCAGCTTAGGCGGTCAGGAGGGAGCTG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TGGTGGTAGGG 665s TGGTGGTAGGG 665s Processing line... 665s --- Summary --- 665s Read 1 reference strings 665s Checked 87 alignments, 0 edits 665s --------------- 665s PASSED 665s Flattened IUPAC characters 665s Mutating sequence Sim.pm.1 665s Introducing 8 SNPs, 0/2 ref/read gaps, and 0 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutating sequence Sim.pm.2 665s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutated reference genome to subject genome 665s SNPs introduced: 10 665s Reference gaps introduced: 1 665s Read gaps introduced: 2 665s Rearrangements introduced: 0 665s Created read sampler 665s Sampling 123 reads 665s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 665s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 665s parsing sequence Sim.pm.1... 665s parsing sequence Sim.pm.2... 665s Parsed 143 reference bases 665s *** Run 20 of 100 665s /usr/bin/bowtie2 --cp-min 15 --score-min L,5.46731078378922,3.55482468156149 --mm --rdg 20.8738259562641 --norc -a --cp-ival 1 --local --mp 5.85246401487824,5.39991081645359 --trim3 7 --nofw -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta 665s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '1' because it was < 2 characters long 665s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '5' because it was < 2 characters long 665s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '24' because it was < 2 characters long 665s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #2 of read '27' because it was < 2 characters long 665s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #2 of read '28' because it was < 2 characters long 665s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 665s Warning: skipping read '32' because it was < 2 characters long 665s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '33' because it was < 2 characters long 665s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '37' because it was < 2 characters long 665s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '38' because it was < 2 characters long 665s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '46' because it was < 2 characters long 665s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '47' because it was < 2 characters long 665s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '49' because it was < 2 characters long 665s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '51' because it was < 2 characters long 665s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '54' because it was < 2 characters long 665s Read 50 alignments... 665s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '85' because it was < 2 characters long 665s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '93' because it was < 2 characters long 665s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '100' because it was < 2 characters long 665s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '102' because it was < 2 characters long 665s Warning: skipping mate #1 of read '103' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '103' because it was < 2 characters long 665s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '106' because it was < 2 characters long 665s Warning: skipping mate #1 of read '108' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '108' because it was < 2 characters long 665s Read 100 alignments... 665s 123 reads; of these: 665s 100 (81.30%) were paired; of these: 665s 100 (100.00%) aligned concordantly 0 times 665s 0 (0.00%) aligned concordantly exactly 1 time 665s 0 (0.00%) aligned concordantly >1 times 665s ---- 665s 100 pairs aligned concordantly 0 times; of these: 665s 0 (0.00%) aligned discordantly 1 time 665s ---- 665s 100 pairs aligned 0 times concordantly or discordantly; of these: 665s 200 mates make up the pairs; of these: 665s 200 (100.00%) aligned 0 times 665s 0 (0.00%) aligned exactly 1 time 665s 0 (0.00%) aligned >1 times 665s 23 (18.70%) were unpaired; of these: 665s 23 (100.00%) aligned 0 times 665s 0 (0.00%) aligned exactly 1 time 665s 0 (0.00%) aligned >1 times 665s 0.00% overall alignment rate 665s Read 150 alignments... 665s Read 200 alignments... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s --- Summary --- 665s Read 1 reference strings 665s Checked 0 alignments, 0 edits 665s --------------- 665s PASSED 665s ALSO checking that bowtie2 and bowtie2-align match up 665s /usr/bin/bowtie2 --cp-min 15 --score-min L,5.46731078378922,3.55482468156149 --mm --rdg 20.8738259562641 --norc -a --cp-ival 1 --local --mp 5.85246401487824,5.39991081645359 --trim3 7 --nofw -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 665s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '1' because it was < 2 characters long 665s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '5' because it was < 2 characters long 665s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '24' because it was < 2 characters long 665s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #2 of read '27' because it was < 2 characters long 665s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #2 of read '28' because it was < 2 characters long 665s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 665s Warning: skipping read '32' because it was < 2 characters long 665s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '33' because it was < 2 characters long 665s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '37' because it was < 2 characters long 665s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '38' because it was < 2 characters long 665s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '46' because it was < 2 characters long 665s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '47' because it was < 2 characters long 665s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '49' because it was < 2 characters long 665s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '51' because it was < 2 characters long 665s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '54' because it was < 2 characters long 665s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '85' because it was < 2 characters long 665s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '93' because it was < 2 characters long 665s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '100' because it was < 2 characters long 665s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '102' because it was < 2 characters long 665s Warning: skipping mate #1 of read '103' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '103' because it was < 2 characters long 665s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '106' because it was < 2 characters long 665s Warning: skipping mate #1 of read '108' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '108' because it was < 2 characters long 665s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 665s 123 reads; of these: 665s 100 (81.30%) were paired; of these: 665s 100 (100.00%) aligned concordantly 0 times 665s 0 (0.00%) aligned concordantly exactly 1 time 665s 0 (0.00%) aligned concordantly >1 times 665s ---- 665s 100 pairs aligned concordantly 0 times; of these: 665s 0 (0.00%) aligned discordantly 1 time 665s ---- 665s 100 pairs aligned 0 times concordantly or discordantly; of these: 665s 200 mates make up the pairs; of these: 665s 200 (100.00%) aligned 0 times 665s 0 (0.00%) aligned exactly 1 time 665s 0 (0.00%) aligned >1 times 665s 23 (18.70%) were unpaired; of these: 665s 23 (100.00%) aligned 0 times 665s 0 (0.00%) aligned exactly 1 time 665s 0 (0.00%) aligned >1 times 665s 0.00% overall alignment rate 665s Flattened IUPAC characters 665s Mutating sequence Sim.pm.2 665s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutating sequence Sim.pm.1 665s Introducing 22 SNPs, 0/3 ref/read gaps, and 3 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutated reference genome to subject genome 665s SNPs introduced: 23 665s Reference gaps introduced: 0 665s Read gaps introduced: 4 665s Rearrangements introduced: 3 665s Created read sampler 665s Sampling 104 reads 665s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 665s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 665s parsing sequence Sim.pm.1... 665s *** Run 21 of 100 665s /usr/bin/bowtie2 --rdg 15.1574466067287,11.9675076232469 --trim3 0 --ma 10.0739938739173 --score-min L,8.82364219706952,4.57969360997619 -i C,3.43667388526596,3.22226753173989 -D 35 --cp-ival 1 --np 4 --cp-min 7 --trim5 9 -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta 665s parsing sequence Sim.pm.2... 665s Parsed 143 reference bases 665s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 665s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '6' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 665s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '14' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 665s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '22' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 665s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '23' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 665s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '29' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 665s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '33' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 665s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '36' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 665s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '42' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 665s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '47' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 665s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '61' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 665s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '64' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 665s Read 50 alignments... 665s Read 100 alignments... 665s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '66' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 665s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '71' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 665s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '82' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 665s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '83' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 665s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '86' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 665s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '88' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 665s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 665s Warning: skipping read '95' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 665s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '96' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 665s Warning: skipping mate #1 of read '98' because length (1) <= # seed mismatches (0) 665s Warning: skipping mate #1 of read '98' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 665s 104 reads; of these: 665s 91 (87.50%) were paired; of these: 665s 90 (98.90%) aligned concordantly 0 times 665s 0 (0.00%) aligned concordantly exactly 1 time 665s 1 (1.10%) aligned concordantly >1 times 665s ---- 665s 90 pairs aligned concordantly 0 times; of these: 665s 0 (0.00%) aligned discordantly 1 time 665s ---- 665s 90 pairs aligned 0 times concordantly or discordantly; of these: 665s 180 mates make up the pairs; of these: 665s 160 (88.89%) aligned 0 times 665s 12 (6.67%) aligned exactly 1 time 665s 8 (4.44%) aligned >1 times 665s 13 (12.50%) were unpaired; of these: 665s 11 (84.62%) aligned 0 times 665s 2 (15.38%) aligned exactly 1 time 665s 0 (0.00%) aligned >1 times 665s 12.31% overall alignment rate 665s Read 150 alignments... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CCGCGGCTCGGTCTGCGCC 665s CCGCGGCTCGGTCTGCGCC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CC 665s CC 665s Processing line... 665s Processing line... 665s AGAGGGTGACA 665s AGAGGGTGACA 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TG 665s TG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GAGAGGGTGACAGAGGCG 665s GAGAGGGTGACAGAGGCG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GCG 665s GCG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GTTGAGAGGGTG 665s GTTGAGAGGGTG 665s Processing line... 665s Processing line... 665s Processing line... 665s GTGGTGTTGAGAGGGTG 665s GTGGTGTTGAGAGGGTG 665s Processing line... 665s Processing line... 665s CGCGGCTCGGTCTGCGCCCAGCTTAGGCGG 665s CGCGGCTCGGTCTGCGCCCAGCTTAGGCGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GCGCCCAGCTTAGGCGGTCA 665s GCGCCCAGCTTAGGCGGTCA 665s Processing line... 665s Processing line... 665s TT 665s TT 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TCGGTCTGCGCCCA 665s TCGGTCTGCGCCCA 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGACTGGCGGGAAGACC 665s GGACTGGCGGGAAGACC 665s Processing line... 665s TGAG 665s TGAG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s *** Run 22 of 100 665s /usr/bin/bowtie2 -D 45 --gbar 6 -R 2 --score-min L,3.76202203369321,1.04233530145069 --np 10 --cp-min 2 --mp 9.15270868361939,5.43907412063391 --trim3 7 --rfg 22.6615686911314,10.4837328540707 --cp-ival 1 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GTGTTG 665s GTGTTG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CGGGAAGACCGCGGCTCGGT 665s CGGGAAGACCGCGGCTCGGT 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s CT 665s CT 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s GGAAGACCGCGGC 665s GGAAGACCGCGGC 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s AG 665s AG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TGGTGGTGGTAGGGGGG 665s TGGTGGTGGTAGGGGGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s AGGCGGTCAGG 665s AGGCGGTCAGG 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s TG 665s TG 665s Processing line... 665s GTGT 665s GTGT 665s Processing line... 665s GTCT 665s GTCT 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s Processing line... 665s --- Summary --- 665s Read 1 reference strings 665s Checked 24 alignments, 0 edits 665s --------------- 665s PASSED 665s Flattened IUPAC characters 665s Mutating sequence Sim.pm.1 665s Introducing 13 SNPs, 0/5 ref/read gaps, and 1 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutating sequence Sim.pm.2 665s Introducing 1 SNPs, 0/3 ref/read gaps, and 2 rearrangements 665s Finished SNPs 665s Finished ref gaps 665s Finished read gaps 665s Mutated reference genome to subject genome 665s SNPs introduced: 14 665s Reference gaps introduced: 0 665s Read gaps introduced: 8 665s Rearrangements introduced: 3 665s Created read sampler 665s Sampling 184 reads 665s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 665s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 665s parsing sequence Sim.pm.1... 665s parsing sequence Sim.pm.2... 665s Parsed 143 reference bases 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_140_140_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_148_148_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_151_151_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_153_153_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_153_153_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_153_153_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_154_154_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_154_154_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_154_154_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_155_155_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_156_156_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_157_157_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_158_158_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_159_159_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_160_160_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_160_160_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_160_160_1/1' because it was < 2 characters long 665s Read 50 alignments... 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_161_161_1/1; setting to 0 instead 665s Read 100 alignments... 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_162_162_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_162_162_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_162_162_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_163_163_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_163_163_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_163_163_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_164_164_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_164_164_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_164_164_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_165_165_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_166_166_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_166_166_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_166_166_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_167_167_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_168_168_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_168_168_1/1' because length (0) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_169_169_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_170_170_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_171_171_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_172_172_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_173_173_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_174_174_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_175_175_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_176_176_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_177_177_1/1; setting to 0 instead 665s Warning: skipping read 'R_1_1_1_177_177_1/1' because length (1) <= # seed mismatches (0) 665s Warning: skipping read 'R_1_1_1_177_177_1/1' because it was < 2 characters long 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_178_178_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_179_179_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_180_180_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_181_181_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_182_182_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_183_183_1/1; setting to 0 instead 665s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_184_184_1/1; setting to 0 instead 665s 184 reads; of these: 665s 184 (100.00%) were unpaired; of these: 665s 145 (78.80%) aligned 0 times 665s 27 (14.67%) aligned exactly 1 time 665s 12 (6.52%) aligned >1 times 665s 21.20% overall alignment rate 665s Read 150 alignments... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTC 666s GTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s CGGTCAG 666s CGGTCAG 666s Processing line... 666s TCGGTCTGCGCCCA 666s TCGGTCTGCGCCCA 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GTTGA 666s GTTGA 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GACC 666s GACC 666s Processing line... 666s Processing line... 666s Processing line... 666s GCGGCTCGGTCTGCGCCC 666s GCGGCTCGGTCTGCGCCC 666s Processing line... 666s GTGGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCT 666s GTGGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCT 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GGGGGGACTGGCGGGAAGACCG 666s GGGGGGACTGGCGGGAAGACCG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GTCTGCGCCC 666s GTCTGCGCCC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s CTGGC 666s CTGGC 666s Processing line... 666s GGGGACTGGCGGGAAGACCGC 666s GGGGACTGGCGGGAAGACCGC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s CGCGGCTCGGTCTGCGCC 666s CGCGGCTCGGTCTGCGCC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s CTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCT 666s CTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCT 666s Processing line... 666s TCCGGGT 666s TCCGGGT 666s Processing line... 666s Processing line... 666s Processing line... 666s GGTC 666s GGTC 666s Processing line... 666s CAGCTTAGGC 666s CAGCTTAGGC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GGTGGT 666s GGTGGT 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s AGCTT 666s AGCTT 666s Processing line... 666s CG 666s CG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s TGC 666s TGC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GTAGGGGGG 666s GTAGGGGGG 666s Processing line... 666s Processing line... 666s GGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCA 666s GGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCA 666s Processing line... 666s GGTCAGGAG 666s GGTCAGGAG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s TCGG 666s TCGG 666s Processing line... 666s Processing line... 666s Processing line... 666s GGTGGTG 666s GGTGGTG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GGGACTGGCGGGAA 666s GGGACTGGCGGGAA 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GTAGGGGGGGACTGGCGGGAAGAC 666s GTAGGGGGGGACTGGCGGGAAGAC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s CGGGAAGACC 666s CGGGAAGACC 666s Processing line... 666s GTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTC 666s GTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GACC 666s GACC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s TCAGGAGG 666s TCAGGAGG 666s Processing line... 666s CGCGGCTCGG 666s CGCGGCTCGG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GGG 666s GGG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s TCGGTCTGCGCCCA 666s TCGGTCTGCGCCCA 666s Processing line... 666s TGGTGG 666s TGGTGG 666s Processing line... 666s Processing line... 666s GAGAG 666s GAGAG 666s Processing line... 666s Processing line... 666s Processing line... 666s TTAGGCGGT 666s TTAGGCGGT 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GT 666s GT 666s Processing line... 666s CCAGC 666s CCAGC 666s Processing line... 666s Processing line... 666s Processing line... 666s --- Summary --- 666s Read 1 reference strings 666s Checked 39 alignments, 0 edits 666s --------------- 666s PASSED 666s ALSO checking that bowtie2 and bowtie2-align match up 666s /usr/bin/bowtie2 -D 45 --gbar 6 -R 2 --score-min L,3.76202203369321,1.04233530145069 --np 10 --cp-min 2 --mp 9.15270868361939,5.43907412063391 --trim3 7 --rfg 22.6615686911314,10.4837328540707 --cp-ival 1 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (1) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_140_140_1/1' because length (1) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_148_148_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_151_151_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_153_153_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_153_153_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_153_153_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_154_154_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_154_154_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_154_154_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_155_155_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_156_156_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_157_157_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_158_158_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_159_159_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_160_160_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_160_160_1/1' because length (1) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_160_160_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_161_161_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_162_162_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_162_162_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_162_162_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_163_163_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_163_163_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_163_163_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_164_164_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_164_164_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_164_164_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_165_165_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_166_166_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_166_166_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_166_166_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_167_167_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_168_168_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_168_168_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_169_169_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_170_170_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_171_171_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_172_172_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_173_173_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_174_174_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_175_175_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_176_176_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_177_177_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_177_177_1/1' because length (1) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_177_177_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_178_178_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_179_179_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_180_180_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_181_181_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_182_182_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_183_183_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_184_184_1/1; setting to 0 instead 666s 184 reads; of these: 666s 184 (100.00%) were unpaired; of these: 666s 145 (78.80%) aligned 0 times 666s 27 (14.67%) aligned exactly 1 time 666s 12 (6.52%) aligned >1 times 666s 21.20% overall alignment rate 666s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 666s /usr/bin/bowtie2 -D 45 --gbar 6 -R 2 --score-min L,3.76202203369321,1.04233530145069 --np 10 --cp-min 2 --mp 9.15270868361939,5.43907412063391 --trim3 7 --rfg 22.6615686911314,10.4837328540707 --cp-ival 1 --qseq -p 2 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 666s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (1) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_140_140_1/1' because length (1) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_148_148_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_151_151_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_153_153_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_153_153_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_153_153_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_154_154_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_154_154_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_154_154_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_155_155_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_156_156_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_157_157_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_158_158_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_159_159_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_160_160_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_160_160_1/1' because length (1) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_160_160_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_161_161_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_162_162_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_162_162_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_162_162_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_163_163_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_163_163_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_163_163_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_164_164_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_164_164_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_164_164_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_165_165_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_166_166_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_166_166_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_166_166_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_167_167_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_168_168_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_168_168_1/1' because length (0) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_169_169_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_170_170_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_171_171_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_172_172_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_173_173_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_174_174_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_175_175_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_176_176_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_177_177_1/1; setting to 0 instead 666s Warning: skipping read 'R_1_1_1_177_177_1/1' because length (1) <= # seed mismatches (0) 666s Warning: skipping read 'R_1_1_1_177_177_1/1' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_178_178_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_179_179_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_180_180_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_181_181_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_182_182_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_183_183_1/1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_184_184_1/1; setting to 0 instead 666s 184 reads; of these: 666s 184 (100.00%) were unpaired; of these: 666s 145 (78.80%) aligned 0 times 666s 27 (14.67%) aligned exactly 1 time 666s 12 (6.52%) aligned >1 times 666s 21.20% overall alignment rate 666s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 666s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 666s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 666s Flattened IUPAC characters 666s Mutating sequence Sim.pm.2 666s Introducing 0 SNPs, 3/0 ref/read gaps, and 1 rearrangements 666s Finished SNPs 666s Finished ref gaps 666s Finished read gaps 666s Mutating sequence Sim.pm.1 666s Introducing 9 SNPs, 0/1 ref/read gaps, and 1 rearrangements 666s Finished SNPs 666s Finished ref gaps 666s Finished read gaps 666s Mutated reference genome to subject genome 666s SNPs introduced: 9 666s Reference gaps introduced: 3 666s Read gaps introduced: 1 666s Rearrangements introduced: 2 666s Created read sampler 666s Sampling 92 reads 666s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 666s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 666s parsing sequence Sim.pm.1... 666s parsing sequence Sim.pm.2... 666s Parsed 143 reference bases 666s *** Run 23 of 100 666s /usr/bin/bowtie2 --np 2 --cp-min 2 --rdg 43.5691200673465 --score-min L,1.20677724274623,7.4829121064616 -D 23 --local --cp-ival 1 -M 4 --norc --n-ceil 1.38300671873408,0.509561897866783 --trim3 7 -i S,0.0785633594160367,1.88039515718519 --mp 9.7037907218664,2.59820593886427 -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta 666s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 666s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '21' because it was < 2 characters long 666s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '25' because it was < 2 characters long 666s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '27' because it was < 2 characters long 666s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 666s Warning: skipping read '38' because it was < 2 characters long 666s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '40' because it was < 2 characters long 666s Warning: skipping mate #2 of read '40' because it was < 2 characters long 666s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '46' because it was < 2 characters long 666s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 666s Warning: skipping read '47' because it was < 2 characters long 666s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 666s Warning: skipping read '55' because it was < 2 characters long 666s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 666s Warning: skipping read '58' because it was < 2 characters long 666s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '66' because it was < 2 characters long 666s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 666s Warning: skipping read '75' because it was < 2 characters long 666s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '79' because it was < 2 characters long 666s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #2 of read '87' because it was < 2 characters long 666s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '90' because it was < 2 characters long 666s Read 50 alignments... 666s Read 100 alignments... 666s 92 reads; of these: 666s 68 (73.91%) were paired; of these: 666s 68 (100.00%) aligned concordantly 0 times 666s 0 (0.00%) aligned concordantly exactly 1 time 666s 0 (0.00%) aligned concordantly >1 times 666s ---- 666s 68 pairs aligned concordantly 0 times; of these: 666s 0 (0.00%) aligned discordantly 1 time 666s ---- 666s 68 pairs aligned 0 times concordantly or discordantly; of these: 666s 136 mates make up the pairs; of these: 666s 136 (100.00%) aligned 0 times 666s 0 (0.00%) aligned exactly 1 time 666s 0 (0.00%) aligned >1 times 666s 24 (26.09%) were unpaired; of these: 666s 24 (100.00%) aligned 0 times 666s 0 (0.00%) aligned exactly 1 time 666s 0 (0.00%) aligned >1 times 666s 0.00% overall alignment rate 666s Read 150 alignments... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s --- Summary --- 666s Read 1 reference strings 666s Checked 0 alignments, 0 edits 666s --------------- 666s PASSED 666s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 666s /usr/bin/bowtie2 --np 2 --cp-min 2 --rdg 43.5691200673465 --score-min L,1.20677724274623,7.4829121064616 -D 23 --local --cp-ival 1 -M 4 --norc --n-ceil 1.38300671873408,0.509561897866783 --trim3 7 -i S,0.0785633594160367,1.88039515718519 --mp 9.7037907218664,2.59820593886427 -f -p 4 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 666s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 666s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '21' because it was < 2 characters long 666s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '25' because it was < 2 characters long 666s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '27' because it was < 2 characters long 666s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 666s Warning: skipping read '38' because it was < 2 characters long 666s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '40' because it was < 2 characters long 666s Warning: skipping mate #2 of read '40' because it was < 2 characters long 666s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '46' because it was < 2 characters long 666s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 666s Warning: skipping read '47' because it was < 2 characters long 666s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 666s Warning: skipping read '55' because it was < 2 characters long 666s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 666s Warning: skipping read '58' because it was < 2 characters long 666s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '66' because it was < 2 characters long 666s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 666s Warning: skipping read '75' because it was < 2 characters long 666s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '79' because it was < 2 characters long 666s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #2 of read '87' because it was < 2 characters long 666s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '90' because it was < 2 characters long 666s 92 reads; of these: 666s 68 (73.91%) were paired; of these: 666s 68 (100.00%) aligned concordantly 0 times 666s 0 (0.00%) aligned concordantly exactly 1 time 666s 0 (0.00%) aligned concordantly >1 times 666s ---- 666s 68 pairs aligned concordantly 0 times; of these: 666s 0 (0.00%) aligned discordantly 1 time 666s ---- 666s 68 pairs aligned 0 times concordantly or discordantly; of these: 666s 136 mates make up the pairs; of these: 666s 136 (100.00%) aligned 0 times 666s 0 (0.00%) aligned exactly 1 time 666s 0 (0.00%) aligned >1 times 666s 24 (26.09%) were unpaired; of these: 666s 24 (100.00%) aligned 0 times 666s 0 (0.00%) aligned exactly 1 time 666s 0 (0.00%) aligned >1 times 666s 0.00% overall alignment rate 666s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 666s Flattened IUPAC characters 666s Mutating sequence Sim.pm.2 666s Introducing 5 SNPs, 0/2 ref/read gaps, and 0 rearrangements 666s Finished SNPs 666s Finished ref gaps 666s Finished read gaps 666s Mutating sequence Sim.pm.1 666s Introducing 2 SNPs, 1/2 ref/read gaps, and 0 rearrangements 666s Finished SNPs 666s Finished ref gaps 666s Finished read gaps 666s Mutated reference genome to subject genome 666s SNPs introduced: 7 666s Reference gaps introduced: 1 666s Read gaps introduced: 4 666s Rearrangements introduced: 0 666s Created read sampler 666s Sampling 175 reads 666s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 666s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 666s parsing sequence Sim.pm.1... 666s parsing sequence Sim.pm.2... 666s Parsed 143 reference bases 666s *** Run 24 of 100 666s /usr/bin/bowtie2 --mp 7.37892108606561,5.09389544463768 --trim3 5 --cp-ival 1 --norc --n-ceil 0.772866375834515,0.807664068253453 --mm --rdg 26.3725254464264,8.39756564506939 --score-min L,8.94078234954109,9.31162672419486 --np 12 --cp-min 2 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 666s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '6' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 666s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '9' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 666s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '12' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 666s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '20' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 666s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '21' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 666s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '23' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 666s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '30' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 666s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '42' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 666s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '47' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 666s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #2 of read '48' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 666s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '51' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 666s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '55' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 666s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '56' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 666s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '58' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 666s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '64' because it was < 2 characters long 666s Read 50 alignments... 666s Read 100 alignments... 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 666s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '72' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 666s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '79' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 666s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '83' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 666s Warning: skipping mate #1 of read '91' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '91' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 666s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '104' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 666s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '128' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 666s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '133' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 666s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '138' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 666s Warning: skipping mate #2 of read '146' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #2 of read '146' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 666s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '151' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 666s Warning: skipping mate #1 of read '152' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #2 of read '152' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '152' because it was < 2 characters long 666s Warning: skipping mate #2 of read '152' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 666s Warning: skipping mate #1 of read '153' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '153' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 666s Warning: skipping mate #1 of read '163' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '163' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 666s Warning: skipping mate #1 of read '165' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '165' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 666s Warning: skipping mate #1 of read '168' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '168' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 666s Warning: skipping mate #1 of read '174' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '174' because it was < 2 characters long 666s Read 150 alignments... 666s Read 200 alignments... 666s 175 reads; of these: 666s 160 (91.43%) were paired; of these: 666s 159 (99.38%) aligned concordantly 0 times 666s 1 (0.62%) aligned concordantly exactly 1 time 666s 0 (0.00%) aligned concordantly >1 times 666s ---- 666s 159 pairs aligned concordantly 0 times; of these: 666s 1 (0.63%) aligned discordantly 1 time 666s ---- 666s 158 pairs aligned 0 times concordantly or discordantly; of these: 666s 316 mates make up the pairs; of these: 666s 283 (89.56%) aligned 0 times 666s 18 (5.70%) aligned exactly 1 time 666s 15 (4.75%) aligned >1 times 666s 15 (8.57%) were unpaired; of these: 666s 14 (93.33%) aligned 0 times 666s 1 (6.67%) aligned exactly 1 time 666s 0 (0.00%) aligned >1 times 666s 11.34% overall alignment rate 666s Read 250 alignments... 666s Read 300 alignments... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GTAG 666s GTAG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GGT 666s GGT 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s CCGCGGCTCGGTC 666s CCGCGGCTCGGTC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s AA 666s AA 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s TGGT 666s TGGT 666s Processing line... 666s Processing line... 666s Processing line... 666s GGGTGACAGAGGC 666s GGGTGACAGAGGC 666s Processing line... 666s Processing line... 666s CTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTT 666s CTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTT 666s Processing line... 666s TGGCGGG 666s TGGCGGG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s CGTGG 666s CGTGG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s AC 666s AC 666s Processing line... 666s Processing line... 666s CT 666s CT 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s CTCGGTCTGCGCCC 666s CTCGGTCTGCGCCC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s TC 666s TC 666s Processing line... 666s Processing line... 666s GGGGGGGACTGGCG 666s GGGGGGGACTGGCG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GGGTGACAGA 666s GGGTGACAGA 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GGGAC 666s GGGAC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s AGGGGGGGACTGGCGGG 666s AGGGGGGGACTGGCGGG 666s Processing line... 666s Processing line... 666s CGGGTGGTG 666s CGGGTGGTG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s TGGTAGGGGGGGACTGGCGGGA 666s TGGTAGGGGGGGACTGGCGGGA 666s Processing line... 666s TGGCGGGAAGA 666s TGGCGGGAAGA 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GT 666s GT 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s TGC 666s TGC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s TGG 666s TGG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s CAG 666s CAG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GGGGGG 666s GGGGGG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s TGGTGGTAGGGGGGGACTGGC 666s TGGTGGTAGGGGGGGACTGGC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GGACTGGCGGGAA 666s GGACTGGCGGGAA 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GT 666s GT 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s CAGCTTAGGCGGTCAGGAGGGAG 666s CAGCTTAGGCGGTCAGGAGGGAG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GAAG 666s GAAG 666s Processing line... 666s TGGT 666s TGGT 666s Processing line... 666s Processing line... 666s Processing line... 666s GGTAGGGGGGGACTGGCGGGAAGA 666s GGTAGGGGGGGACTGGCGGGAAGA 666s Processing line... 666s Processing line... 666s GGGGGGA 666s GGGGGGA 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GGCGTGG 666s GGCGTGG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s TGGCGGGAAGACCGCGGCTCGGTCTGCGCC 666s TGGCGGGAAGACCGCGGCTCGGTCTGCGCC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GG 666s GG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s GGGTGACAGAGGC 666s GGGTGACAGAGGC 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s TGTTGAGAGG 666s TGTTGAGAGG 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s --- Summary --- 666s Read 1 reference strings 666s Checked 38 alignments, 0 edits 666s --------------- 666s PASSED 666s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 666s /usr/bin/bowtie2 --mp 7.37892108606561,5.09389544463768 --trim3 5 --cp-ival 1 --norc --n-ceil 0.772866375834515,0.807664068253453 --mm --rdg 26.3725254464264,8.39756564506939 --score-min L,8.94078234954109,9.31162672419486 --np 12 --cp-min 2 -r -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 666s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '6' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 666s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '9' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 666s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '12' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 666s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '20' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 666s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '21' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 666s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '23' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 666s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '30' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 666s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '42' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 666s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '47' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 666s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #2 of read '48' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 666s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '51' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 666s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '55' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 666s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '64' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 666s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '56' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 666s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '58' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 666s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '83' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 666s Warning: skipping mate #1 of read '91' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '91' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 666s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 666s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '104' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 666s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '128' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 666s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '133' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 666s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '138' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 666s Warning: skipping mate #2 of read '146' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #2 of read '146' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 666s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '151' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 666s Warning: skipping mate #1 of read '152' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #2 of read '152' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '152' because it was < 2 characters long 666s Warning: skipping mate #2 of read '152' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 666s Warning: skipping mate #1 of read '153' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '153' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 666s Warning: skipping mate #1 of read '163' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '163' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 666s Warning: skipping mate #1 of read '165' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '165' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 666s Warning: skipping mate #1 of read '168' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '168' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 666s Warning: skipping mate #1 of read '174' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '174' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 666s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '72' because it was < 2 characters long 666s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 666s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 666s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '79' because it was < 2 characters long 666s 175 reads; of these: 666s 160 (91.43%) were paired; of these: 666s 159 (99.38%) aligned concordantly 0 times 666s 1 (0.62%) aligned concordantly exactly 1 time 666s 0 (0.00%) aligned concordantly >1 times 666s ---- 666s 159 pairs aligned concordantly 0 times; of these: 666s 1 (0.63%) aligned discordantly 1 time 666s ---- 666s 158 pairs aligned 0 times concordantly or discordantly; of these: 666s 316 mates make up the pairs; of these: 666s 283 (89.56%) aligned 0 times 666s 18 (5.70%) aligned exactly 1 time 666s 15 (4.75%) aligned >1 times 666s 15 (8.57%) were unpaired; of these: 666s 14 (93.33%) aligned 0 times 666s 1 (6.67%) aligned exactly 1 time 666s 0 (0.00%) aligned >1 times 666s 11.34% overall alignment rate 666s Flattened IUPAC characters 666s Mutating sequence Sim.pm.2 666s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 666s Finished SNPs 666s Finished ref gaps 666s Finished read gaps 666s Mutating sequence Sim.pm.1 666s Introducing 10 SNPs, 1/0 ref/read gaps, and 5 rearrangements 666s Finished SNPs 666s Finished ref gaps 666s Finished read gaps 666s Mutated reference genome to subject genome 666s SNPs introduced: 12 666s Reference gaps introduced: 1 666s Read gaps introduced: 0 666s Rearrangements introduced: 6 666s *** Run 25 of 100 666s /usr/bin/bowtie2 --trim5 2 --cp-min 5 --cp-ival 1 --local -k 2 -N 0 -L31 --score-min L,1.58474610964927,5.5993307302441 --trim3 0 --nofw --mm --rfg 9.97210457205255,15.7102302617252 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 666s Created read sampler 666s Sampling 84 reads 666s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 666s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 666s parsing sequence Sim.pm.1... 666s parsing sequence Sim.pm.2... 666s Parsed 143 reference bases 666s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '3' because it was < 2 characters long 666s Warning: skipping mate #1 of read '6' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '6' because it was < 2 characters long 666s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '14' because it was < 2 characters long 666s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '15' because it was < 2 characters long 666s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '39' because it was < 2 characters long 666s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '48' because it was < 2 characters long 666s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '53' because it was < 2 characters long 666s Warning: skipping mate #2 of read '70' because length (1) <= # seed mismatches (0) 666s Read 50 alignments... 666s Warning: skipping mate #2 of read '70' because it was < 2 characters long 666s 84 reads; of these: 666s 84 (100.00%) were paired; of these: 666s 84 (100.00%) aligned concordantly 0 times 666s 0 (0.00%) aligned concordantly exactly 1 time 666s 0 (0.00%) aligned concordantly >1 times 666s ---- 666s 84 pairs aligned concordantly 0 times; of these: 666s 0 (0.00%) aligned discordantly 1 time 666s ---- 666s 84 pairs aligned 0 times concordantly or discordantly; of these: 666s 168 mates make up the pairs; of these: 666s 168 (100.00%) aligned 0 times 666s 0 (0.00%) aligned exactly 1 time 666s 0 (0.00%) aligned >1 times 666s 0.00% overall alignment rate 666s Read 100 alignments... 666s Read 150 alignments... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s --- Summary --- 666s Read 1 reference strings 666s Checked 0 alignments, 0 edits 666s --------------- 666s PASSED 666s Flattened IUPAC characters 666s Mutating sequence Sim.pm.2 666s Introducing 5 SNPs, 1/3 ref/read gaps, and 0 rearrangements 666s Finished SNPs 666s Finished ref gaps 666s Finished read gaps 666s Mutating sequence Sim.pm.1 666s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 666s Finished SNPs 666s Finished ref gaps 666s Finished read gaps 666s Mutated reference genome to subject genome 666s SNPs introduced: 8 666s Reference gaps introduced: 1 666s Read gaps introduced: 3 666s Rearrangements introduced: 0 666s Created read sampler 666s Sampling 44 reads 666s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 666s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 666s parsing sequence Sim.pm.1... 666s parsing sequence Sim.pm.2... 666s Parsed 143 reference bases 666s *** Run 26 of 100 666s /usr/bin/bowtie2 --score-min L,4.00791811881263,3.88895461734438 --mp 4.84328413227534,1.2043580242295 -i S,1.87020449105994 -R 3 -D 34 --rfg 25.0492547909667 --mm --cp-min 8 -M 2 --local --cp-ival 1 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 666s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 666s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '13' because it was < 2 characters long 666s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '19' because it was < 2 characters long 666s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #2 of read '40' because it was < 2 characters long 666s 44 reads; of these: 666s 44 (100.00%) were paired; of these: 666s 44 (100.00%) aligned concordantly 0 times 666s 0 (0.00%) aligned concordantly exactly 1 time 666s 0 (0.00%) aligned concordantly >1 times 666s ---- 666s 44 pairs aligned concordantly 0 times; of these: 666s 0 (0.00%) aligned discordantly 1 time 666s ---- 666s 44 pairs aligned 0 times concordantly or discordantly; of these: 666s 88 mates make up the pairs; of these: 666s 88 (100.00%) aligned 0 times 666s 0 (0.00%) aligned exactly 1 time 666s 0 (0.00%) aligned >1 times 666s 0.00% overall alignment rate 666s Read 50 alignments... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s Processing line... 666s --- Summary --- 666s Read 1 reference strings 666s Checked 0 alignments, 0 edits 666s --------------- 666s PASSED 666s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 666s /usr/bin/bowtie2 --score-min L,4.00791811881263,3.88895461734438 --mp 4.84328413227534,1.2043580242295 -i S,1.87020449105994 -R 3 -D 34 --rfg 25.0492547909667 --mm --cp-min 8 -M 2 --local --cp-ival 1 -r -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 666s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 666s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '13' because it was < 2 characters long 666s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #1 of read '19' because it was < 2 characters long 666s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 666s Warning: skipping mate #2 of read '40' because it was < 2 characters long 666s 44 reads; of these: 666s 44 (100.00%) were paired; of these: 666s 44 (100.00%) aligned concordantly 0 times 666s 0 (0.00%) aligned concordantly exactly 1 time 666s 0 (0.00%) aligned concordantly >1 times 666s ---- 666s 44 pairs aligned concordantly 0 times; of these: 666s 0 (0.00%) aligned discordantly 1 time 666s ---- 666s 44 pairs aligned 0 times concordantly or discordantly; of these: 666s 88 mates make up the pairs; of these: 666s 88 (100.00%) aligned 0 times 666s 0 (0.00%) aligned exactly 1 time 666s 0 (0.00%) aligned >1 times 666s 0.00% overall alignment rate 666s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 666s Flattened IUPAC characters 666s Mutating sequence Sim.pm.2 666s Introducing 14 SNPs, 0/0 ref/read gaps, and 0 rearrangements 666s Finished SNPs 666s Finished ref gaps 666s Finished read gaps 666s Mutating sequence Sim.pm.1 666s Introducing 14 SNPs, 2/1 ref/read gaps, and 1 rearrangements 666s Finished SNPs 666s Finished ref gaps 666s Finished read gaps 666s Mutated reference genome to subject genome 666s SNPs introduced: 28 666s Reference gaps introduced: 2 666s Read gaps introduced: 1 666s Rearrangements introduced: 1 666s Created read sampler 666s Sampling 116 reads 666s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 666s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 666s parsing sequence Sim.pm.1... 666s parsing sequence Sim.pm.2... 666s Parsed 143 reference bases 666s *** Run 27 of 100 666s /usr/bin/bowtie2 -a --local --cp-ival 1 -N 1 -L16 --mp 6.81615006009711,1.70652343288739 --rfg 9.55608479365111 --np 11 --cp-min 2 --score-min L,1.51392638016666,2.8389284826391 --rdg 45.1507309907173,17.6374590998441 --mm -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 667s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #2 of read '21' because it was < 2 characters long 667s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #2 of read '41' because it was < 2 characters long 667s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '64' because it was < 2 characters long 667s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #2 of read '75' because it was < 2 characters long 667s Read 50 alignments... 667s Read 100 alignments... 667s Read 150 alignments... 667s 116 reads; of these: 667s 116 (100.00%) were paired; of these: 667s 116 (100.00%) aligned concordantly 0 times 667s 0 (0.00%) aligned concordantly exactly 1 time 667s 0 (0.00%) aligned concordantly >1 times 667s ---- 667s 116 pairs aligned concordantly 0 times; of these: 667s 0 (0.00%) aligned discordantly 1 time 667s ---- 667s 116 pairs aligned 0 times concordantly or discordantly; of these: 667s 232 mates make up the pairs; of these: 667s 232 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 0.00% overall alignment rate 667s Read 200 alignments... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s --- Summary --- 667s Read 1 reference strings 667s Checked 0 alignments, 0 edits 667s --------------- 667s PASSED 667s Flattened IUPAC characters 667s Mutating sequence Sim.pm.2 667s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 667s Finished SNPs 667s Finished ref gaps 667s Finished read gaps 667s Mutating sequence Sim.pm.1 667s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 667s Finished SNPs 667s Finished ref gaps 667s Finished read gaps 667s Mutated reference genome to subject genome 667s SNPs introduced: 10 667s Reference gaps introduced: 0 667s Read gaps introduced: 1 667s Rearrangements introduced: 0 667s Created read sampler 667s Sampling 61 reads 667s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 667s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 667s parsing sequence Sim.pm.1... 667s parsing sequence Sim.pm.2... 667s Parsed 143 reference bases 667s *** Run 28 of 100 667s /usr/bin/bowtie2 --rfg 19.1405713418259 --nofw --trim3 2 -N 0 -L29 --local --cp-ival 1 --trim5 0 --n-ceil 0.177633455069197,0.811254334383001 --rdg 1.09865255206147 --mm --score-min L,3.92045948944942,9.95352557210702 --gbar 2 --np 2 --cp-min 2 -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta 667s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '18' because it was < 2 characters long 667s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '23' because it was < 2 characters long 667s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '27' because it was < 2 characters long 667s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '38' because it was < 2 characters long 667s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '42' because it was < 2 characters long 667s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '52' because it was < 2 characters long 667s Warning: skipping mate #1 of read '61' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '61' because it was < 2 characters long 667s 61 reads; of these: 667s 57 (93.44%) were paired; of these: 667s 57 (100.00%) aligned concordantly 0 times 667s 0 (0.00%) aligned concordantly exactly 1 time 667s 0 (0.00%) aligned concordantly >1 times 667s ---- 667s 57 pairs aligned concordantly 0 times; of these: 667s 0 (0.00%) aligned discordantly 1 time 667s ---- 667s 57 pairs aligned 0 times concordantly or discordantly; of these: 667s 114 mates make up the pairs; of these: 667s 114 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 4 (6.56%) were unpaired; of these: 667s 4 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 0.00% overall alignment rate 667s Read 50 alignments... 667s Read 100 alignments... 667s Processing line... 667s Processing line... 667s Processing line... 667s /usr/bin/bowtie2 --rfg 19.1405713418259 --nofw --trim3 2 -N 0 -L29 --local --cp-ival 1 --trim5 0 --n-ceil 0.177633455069197,0.811254334383001 --rdg 1.09865255206147 --mm --score-min L,3.92045948944942,9.95352557210702 --gbar 2 --np 2 --cp-min 2 -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s --- Summary --- 667s Read 1 reference strings 667s Checked 0 alignments, 0 edits 667s --------------- 667s PASSED 667s ALSO checking that bowtie2 and bowtie2-align match up 667s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '18' because it was < 2 characters long 667s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '23' because it was < 2 characters long 667s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '27' because it was < 2 characters long 667s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '38' because it was < 2 characters long 667s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '42' because it was < 2 characters long 667s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '52' because it was < 2 characters long 667s Warning: skipping mate #1 of read '61' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '61' because it was < 2 characters long 667s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 667s 61 reads; of these: 667s 57 (93.44%) were paired; of these: 667s 57 (100.00%) aligned concordantly 0 times 667s 0 (0.00%) aligned concordantly exactly 1 time 667s 0 (0.00%) aligned concordantly >1 times 667s ---- 667s 57 pairs aligned concordantly 0 times; of these: 667s 0 (0.00%) aligned discordantly 1 time 667s ---- 667s 57 pairs aligned 0 times concordantly or discordantly; of these: 667s 114 mates make up the pairs; of these: 667s 114 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 4 (6.56%) were unpaired; of these: 667s 4 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 0.00% overall alignment rate 667s /usr/bin/bowtie2 --rfg 19.1405713418259 --nofw --trim3 2 -N 0 -L29 --local --cp-ival 1 --trim5 0 --n-ceil 0.177633455069197,0.811254334383001 --rdg 1.09865255206147 --mm --score-min L,3.92045948944942,9.95352557210702 --gbar 2 --np 2 --cp-min 2 -f -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 667s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 667s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '18' because it was < 2 characters long 667s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '23' because it was < 2 characters long 667s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '27' because it was < 2 characters long 667s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '38' because it was < 2 characters long 667s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '42' because it was < 2 characters long 667s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '52' because it was < 2 characters long 667s Warning: skipping mate #1 of read '61' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '61' because it was < 2 characters long 667s 61 reads; of these: 667s 57 (93.44%) were paired; of these: 667s 57 (100.00%) aligned concordantly 0 times 667s 0 (0.00%) aligned concordantly exactly 1 time 667s 0 (0.00%) aligned concordantly >1 times 667s ---- 667s 57 pairs aligned concordantly 0 times; of these: 667s 0 (0.00%) aligned discordantly 1 time 667s ---- 667s 57 pairs aligned 0 times concordantly or discordantly; of these: 667s 114 mates make up the pairs; of these: 667s 114 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 4 (6.56%) were unpaired; of these: 667s 4 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 0.00% overall alignment rate 667s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 667s Flattened IUPAC characters 667s Mutating sequence Sim.pm.2 667s Introducing 10 SNPs, 1/1 ref/read gaps, and 0 rearrangements 667s Finished SNPs 667s Finished ref gaps 667s Finished read gaps 667s Mutating sequence Sim.pm.1 667s Introducing 0 SNPs, 0/3 ref/read gaps, and 1 rearrangements 667s Finished SNPs 667s Finished ref gaps 667s Finished read gaps 667s Mutated reference genome to subject genome 667s SNPs introduced: 10 667s Reference gaps introduced: 1 667s Read gaps introduced: 4 667s Rearrangements introduced: 1 667s Created read sampler 667s Sampling 35 reads 667s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 667s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 667s *** Run 29 of 100 667s /usr/bin/bowtie2 --cp-min 4 --cp-ival 3 -R 2 --score-min L,2.84222870626926,6.19837744015366 --ma 1.62137487568747 --mm --rdg 2.71964357661535 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 667s parsing sequence Sim.pm.1... 667s parsing sequence Sim.pm.2... 667s Parsed 143 reference bases 667s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 667s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '7' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 667s 35 reads; of these: 667s 35 (100.00%) were paired; of these: 667s 34 (97.14%) aligned concordantly 0 times 667s 0 (0.00%) aligned concordantly exactly 1 time 667s 1 (2.86%) aligned concordantly >1 times 667s ---- 667s 34 pairs aligned concordantly 0 times; of these: 667s 1 (2.94%) aligned discordantly 1 time 667s ---- 667s 33 pairs aligned 0 times concordantly or discordantly; of these: 667s 66 mates make up the pairs; of these: 667s 57 (86.36%) aligned 0 times 667s 4 (6.06%) aligned exactly 1 time 667s 5 (7.58%) aligned >1 times 667s 18.57% overall alignment rate 667s Read 50 alignments... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s CTGGTGGTGGTAGG 667s CTGGTGGTGGTAGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GG 667s GG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GTTGAGAGGGTGACAGA 667s GTTGAGAGGGTGACAGA 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s CT 667s CT 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TGG 667s TGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TCA 667s TCA 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TGGTGGTAG 667s TGGTGGTAG 667s Processing line... 667s GGTGGTA 667s GGTGGTA 667s Processing line... 667s TAGGGGGGGAC 667s TAGGGGGGGAC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GG 667s GG 667s Processing line... 667s TG 667s TG 667s Processing line... 667s GTGGTGTTG 667s GTGGTGTTG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TTGAGAGG 667s TTGAGAGG 667s Processing line... 667s --- Summary --- 667s Read 1 reference strings 667s Checked 13 alignments, 0 edits 667s /usr/bin/bowtie2 --cp-min 4 --cp-ival 3 -R 2 --score-min L,2.84222870626926,6.19837744015366 --ma 1.62137487568747 --mm --rdg 2.71964357661535 -r -p 2 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 667s --------------- 667s PASSED 667s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 667s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 667s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '7' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 667s 35 reads; of these: 667s 35 (100.00%) were paired; of these: 667s 34 (97.14%) aligned concordantly 0 times 667s 0 (0.00%) aligned concordantly exactly 1 time 667s 1 (2.86%) aligned concordantly >1 times 667s ---- 667s 34 pairs aligned concordantly 0 times; of these: 667s 1 (2.94%) aligned discordantly 1 time 667s ---- 667s 33 pairs aligned 0 times concordantly or discordantly; of these: 667s 66 mates make up the pairs; of these: 667s 57 (86.36%) aligned 0 times 667s 4 (6.06%) aligned exactly 1 time 667s 5 (7.58%) aligned >1 times 667s 18.57% overall alignment rate 667s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 667s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 667s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 667s Flattened IUPAC characters 667s Mutating sequence Sim.pm.1 667s Introducing 21 SNPs, 4/0 ref/read gaps, and 0 rearrangements 667s Finished SNPs 667s Finished ref gaps 667s Finished read gaps 667s Mutating sequence Sim.pm.2 667s Introducing 0 SNPs, 1/1 ref/read gaps, and 1 rearrangements 667s Finished SNPs 667s Finished ref gaps 667s Finished read gaps 667s Mutated reference genome to subject genome 667s SNPs introduced: 21 667s Reference gaps introduced: 5 667s Read gaps introduced: 1 667s Rearrangements introduced: 1 667s Created read sampler 667s Sampling 184 reads 667s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 667s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 667s parsing sequence Sim.pm.1... 667s parsing sequence Sim.pm.2... 667s Parsed 143 reference bases 667s *** Run 30 of 100 667s /usr/bin/bowtie2 -D 19 --score-min L,9.16696983445084,2.52364601963661 --trim3 6 --rfg 25.854191173616 --mm --cp-min 8 --cp-ival 1 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 667s Read 50 alignments... 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 667s Warning: skipping mate #2 of read 'R_1_1_1_125_125_1/1' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_149_149_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_149_149_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_151_151_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_157_157_1/1' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_157_157_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_163_163_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_163_163_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_164_164_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_164_164_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_169_169_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_169_169_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_175_175_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_176_176_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_176_176_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_176_176_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_176_176_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_182_182_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_182_182_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_183_183_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_183_183_1/1; setting to 0 instead 667s Warning: skipping mate #1 of read 'R_1_1_1_183_183_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read 'R_1_1_1_183_183_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_184_184_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_184_184_1/1; setting to 0 instead 667s Read 100 alignments... 667s 184 reads; of these: 667s 170 (92.39%) were paired; of these: 667s 167 (98.24%) aligned concordantly 0 times 667s 0 (0.00%) aligned concordantly exactly 1 time 667s 3 (1.76%) aligned concordantly >1 times 667s ---- 667s 167 pairs aligned concordantly 0 times; of these: 667s 1 (0.60%) aligned discordantly 1 time 667s ---- 667s 166 pairs aligned 0 times concordantly or discordantly; of these: 667s 332 mates make up the pairs; of these: 667s 287 (86.45%) aligned 0 times 667s 28 (8.43%) aligned exactly 1 time 667s 17 (5.12%) aligned >1 times 667s 14 (7.61%) were unpaired; of these: 667s 14 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 14.97% overall alignment rate 667s Read 150 alignments... 667s Read 200 alignments... 667s Read 250 alignments... 667s Read 300 alignments... 667s Read 350 alignments... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TT 667s TT 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GTTGAG 667s GTTGAG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GCCCAGC 667s GCCCAGC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GTGACAGAGGC 667s GTGACAGAGGC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGTG 667s GGTG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s CC 667s CC 667s Processing line... 667s Processing line... 667s GTGGTG 667s GTGGTG 667s Processing line... 667s Processing line... 667s GGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGG 667s GGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGGAAGACCGCGGCTC 667s GGGAAGACCGCGGCTC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s AGGGTGA 667s AGGGTGA 667s Processing line... 667s Processing line... 667s GAAGAC 667s GAAGAC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GTGGTAGGGGGG 667s GTGGTAGGGGGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TGAGAG 667s TGAGAG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s CCGGG 667s CCGGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s AGG 667s AGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGG 667s GGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GAGGCG 667s GAGGCG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGCGGTC 667s GGCGGTC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s CGG 667s CGG 667s Processing line... 667s Processing line... 667s TGG 667s TGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGTGTTGAGA 667s GGTGTTGAGA 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGGGGGG 667s GGGGGGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TGG 667s TGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TCGG 667s TCGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s CTTAGGCGGTC 667s CTTAGGCGGTC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s CAGCTTAG 667s CAGCTTAG 667s Processing line... 667s GGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAG 667s GGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAG 667s Processing line... 667s AGAGGCGT 667s AGAGGCGT 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TGCGCCCAGCTTAGGCGGTCAGGAGGGA 667s TGCGCCCAGCTTAGGCGGTCAGGAGGGA 667s Processing line... 667s Processing line... 667s GGCGGTCAGGAGGGAGC 667s GGCGGTCAGGAGGGAGC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TGCGCCCAG 667s TGCGCCCAG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TCCGGGTGGTGTTG 667s TCCGGGTGGTGTTG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s AG 667s AG 667s Processing line... 667s TGGTGGT 667s TGGTGGT 667s Processing line... 667s GGAA 667s GGAA 667s Processing line... 667s Processing line... 667s CTGGTGGTGGTAG 667s CTGGTGGTGGTAG 667s Processing line... 667s AG 667s AG 667s Processing line... 667s Processing line... 667s Processing line... 667s GGGGGGGACTGGCGGGAAGACCG 667s GGGGGGGACTGGCGGGAAGACCG 667s Processing line... 667s Processing line... 667s GTC 667s GTC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGCGGTCAGGAG 667s GGCGGTCAGGAG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s AGAC 667s AGAC 667s Processing line... 667s CCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGG 667s CCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGG 667s Processing line... 667s Processing line... 667s GGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGC 667s GGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TGGTAGGGGGGGACTG 667s TGGTAGGGGGGGACTG 667s Processing line... 667s Processing line... 667s TTGAGA 667s TTGAGA 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGTCAGG 667s GGTCAGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGT 667s GGT 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GAAGACCGCGGCTC 667s GAAGACCGCGGCTC 667s Processing line... 667s CGC 667s CGC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GTGGTAGGGGGGGACT 667s GTGGTAGGGGGGGACT 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s CGGGTG 667s CGGGTG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGG 667s GTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGGACTGGCGGGAAGACCGCGGCTCGGTCT 667s GGGACTGGCGGGAAGACCGCGGCTCGGTCT 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s --- Summary --- 667s Read 1 reference strings 667s Checked 53 alignments, 0 edits 667s --------------- 667s PASSED 667s Flattened IUPAC characters 667s *** Run 31 of 100 667s /usr/bin/bowtie2 --norc --cp-ival 4 --local --mp 9.59216708984887,6.69597003849105 --trim3 3 --rfg 26.5076725879461,11.157965494053 --cp-min 2 -R 3 --gbar 1 -D 48 --score-min L,6.28213782281695,9.88376878533529 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 667s Mutating sequence Sim.pm.2 667s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 667s Finished SNPs 667s Finished ref gaps 667s Finished read gaps 667s Mutating sequence Sim.pm.1 667s Introducing 12 SNPs, 2/1 ref/read gaps, and 1 rearrangements 667s Finished SNPs 667s Finished ref gaps 667s Finished read gaps 667s Mutated reference genome to subject genome 667s SNPs introduced: 19 667s Reference gaps introduced: 2 667s Read gaps introduced: 1 667s Rearrangements introduced: 1 667s Created read sampler 667s Sampling 90 reads 667s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 667s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 667s parsing sequence Sim.pm.1... 667s parsing sequence Sim.pm.2... 667s Parsed 143 reference bases 667s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '8' because it was < 2 characters long 667s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '15' because it was < 2 characters long 667s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '17' because it was < 2 characters long 667s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '18' because it was < 2 characters long 667s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '21' because it was < 2 characters long 667s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '23' because it was < 2 characters long 667s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '30' because it was < 2 characters long 667s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '38' because it was < 2 characters long 667s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '46' because it was < 2 characters long 667s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '47' because it was < 2 characters long 667s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '52' because it was < 2 characters long 667s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '54' because it was < 2 characters long 667s Warning: skipping mate #1 of read '58' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '58' because it was < 2 characters long 667s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '65' because it was < 2 characters long 667s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '68' because it was < 2 characters long 667s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '70' because it was < 2 characters long 667s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '74' because it was < 2 characters long 667s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 667s Read 50 alignments... 667s Warning: skipping mate #1 of read '81' because it was < 2 characters long 667s 90 reads; of these: 667s 86 (95.56%) were paired; of these: 667s 86 (100.00%) aligned concordantly 0 times 667s 0 (0.00%) aligned concordantly exactly 1 time 667s 0 (0.00%) aligned concordantly >1 times 667s ---- 667s 86 pairs aligned concordantly 0 times; of these: 667s 0 (0.00%) aligned discordantly 1 time 667s ---- 667s 86 pairs aligned 0 times concordantly or discordantly; of these: 667s 172 mates make up the pairs; of these: 667s 172 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 4 (4.44%) were unpaired; of these: 667s 4 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 0.00% overall alignment rate 667s Read 100 alignments... 667s Read 150 alignments... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s --- Summary --- 667s Read 1 reference strings 667s Checked 0 alignments, 0 edits 667s --------------- 667s PASSED 667s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 667s /usr/bin/bowtie2 --norc --cp-ival 4 --local --mp 9.59216708984887,6.69597003849105 --trim3 3 --rfg 26.5076725879461,11.157965494053 --cp-min 2 -R 3 --gbar 1 -D 48 --score-min L,6.28213782281695,9.88376878533529 -r -p 2 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 667s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '8' because it was < 2 characters long 667s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '15' because it was < 2 characters long 667s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '17' because it was < 2 characters long 667s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '18' because it was < 2 characters long 667s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '21' because it was < 2 characters long 667s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '23' because it was < 2 characters long 667s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '30' because it was < 2 characters long 667s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '38' because it was < 2 characters long 667s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '46' because it was < 2 characters long 667s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '47' because it was < 2 characters long 667s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '52' because it was < 2 characters long 667s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '54' because it was < 2 characters long 667s Warning: skipping mate #1 of read '58' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '58' because it was < 2 characters long 667s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 667s Warning: skipping mate #2 of read '65' because it was < 2 characters long 667s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '68' because it was < 2 characters long 667s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '70' because it was < 2 characters long 667s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '74' because it was < 2 characters long 667s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 667s Warning: skipping mate #1 of read '81' because it was < 2 characters long 667s 90 reads; of these: 667s 86 (95.56%) were paired; of these: 667s 86 (100.00%) aligned concordantly 0 times 667s 0 (0.00%) aligned concordantly exactly 1 time 667s 0 (0.00%) aligned concordantly >1 times 667s ---- 667s 86 pairs aligned concordantly 0 times; of these: 667s 0 (0.00%) aligned discordantly 1 time 667s ---- 667s 86 pairs aligned 0 times concordantly or discordantly; of these: 667s 172 mates make up the pairs; of these: 667s 172 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 4 (4.44%) were unpaired; of these: 667s 4 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 0.00% overall alignment rate 667s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 667s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 667s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 667s Flattened IUPAC characters 667s Mutating sequence Sim.pm.1 667s Introducing 17 SNPs, 1/2 ref/read gaps, and 1 rearrangements 667s Finished SNPs 667s Finished ref gaps 667s Finished read gaps 667s Mutating sequence Sim.pm.2 667s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 667s Finished SNPs 667s Finished ref gaps 667s Finished read gaps 667s Mutated reference genome to subject genome 667s SNPs introduced: 22 667s Reference gaps introduced: 2 667s Read gaps introduced: 2 667s Rearrangements introduced: 1 667s Created read sampler 667s Sampling 101 reads 667s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 667s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 667s parsing sequence Sim.pm.1... 667s parsing sequence Sim.pm.2... 667s Parsed 143 reference bases 667s *** Run 32 of 100 667s /usr/bin/bowtie2 --cp-min 5 --trim5 8 --local --cp-ival 1 --score-min L,9.48332806447655,9.89966920179868 -N 1 -L19 --mp 6.33437833814982,4.72376806220053 --rdg 49.5947747018914,9.16648648965701 --mm -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 667s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 667s Warning: skipping read '3' because it was < 2 characters long 667s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '4' because it was < 2 characters long 667s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #2 of read '7' because it was < 2 characters long 667s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '9' because it was < 2 characters long 667s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 667s Warning: skipping read '12' because it was < 2 characters long 667s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '23' because it was < 2 characters long 667s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #2 of read '28' because it was < 2 characters long 667s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '29' because it was < 2 characters long 667s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '38' because it was < 2 characters long 667s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '44' because it was < 2 characters long 667s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '59' because it was < 2 characters long 667s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #2 of read '73' because it was < 2 characters long 667s Warning: skipping read '76' because length (0) <= # seed mismatches (1) 667s Warning: skipping read '76' because it was < 2 characters long 667s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 667s Warning: skipping read '77' because it was < 2 characters long 667s Read 50 alignments... 667s Warning: skipping mate #1 of read '80' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '80' because it was < 2 characters long 667s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '83' because it was < 2 characters long 667s Warning: skipping read '84' because length (0) <= # seed mismatches (1) 667s Warning: skipping read '84' because it was < 2 characters long 667s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '87' because it was < 2 characters long 667s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '89' because it was < 2 characters long 667s Warning: skipping mate #1 of read '90' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '90' because it was < 2 characters long 667s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '93' because it was < 2 characters long 667s Read 100 alignments... 667s 101 reads; of these: 667s 88 (87.13%) were paired; of these: 667s 88 (100.00%) aligned concordantly 0 times 667s 0 (0.00%) aligned concordantly exactly 1 time 667s 0 (0.00%) aligned concordantly >1 times 667s ---- 667s 88 pairs aligned concordantly 0 times; of these: 667s 0 (0.00%) aligned discordantly 1 time 667s ---- 667s 88 pairs aligned 0 times concordantly or discordantly; of these: 667s 176 mates make up the pairs; of these: 667s 176 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 13 (12.87%) were unpaired; of these: 667s 13 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 0.00% overall alignment rate 667s Read 150 alignments... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s --- Summary --- 667s Read 1 reference strings 667s Checked 0 alignments, 0 edits 667s --------------- 667s PASSED 667s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 667s /usr/bin/bowtie2 --cp-min 5 --trim5 8 --local --cp-ival 1 --score-min L,9.48332806447655,9.89966920179868 -N 1 -L19 --mp 6.33437833814982,4.72376806220053 --rdg 49.5947747018914,9.16648648965701 --mm -r -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 667s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 667s Warning: skipping read '3' because it was < 2 characters long 667s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '4' because it was < 2 characters long 667s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #2 of read '7' because it was < 2 characters long 667s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '9' because it was < 2 characters long 667s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 667s Warning: skipping read '12' because it was < 2 characters long 667s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '23' because it was < 2 characters long 667s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #2 of read '28' because it was < 2 characters long 667s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '29' because it was < 2 characters long 667s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '38' because it was < 2 characters long 667s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '44' because it was < 2 characters long 667s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '59' because it was < 2 characters long 667s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #2 of read '73' because it was < 2 characters long 667s Warning: skipping read '76' because length (0) <= # seed mismatches (1) 667s Warning: skipping read '76' because it was < 2 characters long 667s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 667s Warning: skipping read '77' because it was < 2 characters long 667s Warning: skipping mate #1 of read '80' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '80' because it was < 2 characters long 667s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '83' because it was < 2 characters long 667s Warning: skipping read '84' because length (0) <= # seed mismatches (1) 667s Warning: skipping read '84' because it was < 2 characters long 667s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '87' because it was < 2 characters long 667s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '89' because it was < 2 characters long 667s Warning: skipping mate #1 of read '90' because length (1) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '90' because it was < 2 characters long 667s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (1) 667s Warning: skipping mate #1 of read '93' because it was < 2 characters long 667s 101 reads; of these: 667s 88 (87.13%) were paired; of these: 667s 88 (100.00%) aligned concordantly 0 times 667s 0 (0.00%) aligned concordantly exactly 1 time 667s 0 (0.00%) aligned concordantly >1 times 667s ---- 667s 88 pairs aligned concordantly 0 times; of these: 667s 0 (0.00%) aligned discordantly 1 time 667s ---- 667s 88 pairs aligned 0 times concordantly or discordantly; of these: 667s 176 mates make up the pairs; of these: 667s 176 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 13 (12.87%) were unpaired; of these: 667s 13 (100.00%) aligned 0 times 667s 0 (0.00%) aligned exactly 1 time 667s 0 (0.00%) aligned >1 times 667s 0.00% overall alignment rate 667s Flattened IUPAC characters 667s Mutating sequence Sim.pm.1 667s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 667s Finished SNPs 667s Finished ref gaps 667s Finished read gaps 667s Mutating sequence Sim.pm.2 667s Introducing 9 SNPs, 0/0 ref/read gaps, and 2 rearrangements 667s Finished SNPs 667s Finished ref gaps 667s Finished read gaps 667s Mutated reference genome to subject genome 667s SNPs introduced: 17 667s Reference gaps introduced: 0 667s Read gaps introduced: 0 667s Rearrangements introduced: 3 667s Created read sampler 667s Sampling 139 reads 667s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 667s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 667s parsing sequence Sim.pm.1... 667s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 667s *** Run 33 of 100 667s /usr/bin/bowtie2 --rdg 14.3641351209728 --mm --score-min L,2.19987137661738,1.22568742054674 --ma 35.2106722122557 -D 27 --cp-min 3 --np 4 -i S,2.25292960624165 --cp-ival 1 -M 6 --trim5 9 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq 667s parsing sequence Sim.pm.2... 667s Parsed 143 reference bases 667s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 667s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (1) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 667s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 667s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 667s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 667s Read 50 alignments... 667s 139 reads; of these: 667s 139 (100.00%) were unpaired; of these: 667s 116 (83.45%) aligned 0 times 667s 11 (7.91%) aligned exactly 1 time 667s 12 (8.63%) aligned >1 times 667s 16.55% overall alignment rate 667s Read 100 alignments... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s ACTGGCGGGAAGACCG 667s ACTGGCGGGAAGACCG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGTGG 667s GGTGG 667s Processing line... 667s Processing line... 667s GGTGGTAGGGGGGG 667s GGTGGTAGGGGGGG 667s Processing line... 667s Processing line... 667s GA 667s GA 667s Processing line... 667s AGAGG 667s AGAGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s CTGG 667s CTGG 667s Processing line... 667s Processing line... 667s AGA 667s AGA 667s Processing line... 667s Processing line... 667s CCGGG 667s CCGGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGT 667s GGT 667s Processing line... 667s Processing line... 667s GGGA 667s GGGA 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGTGGTAGGGG 667s GGTGGTAGGGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TGC 667s TGC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s AGGGGGGGACTGGCGGGAAGACCGCGG 667s AGGGGGGGACTGGCGGGAAGACCGCGG 667s Processing line... 667s Processing line... 667s ACCGCG 667s ACCGCG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s CAGAG 667s CAGAG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GGTGGTGGTAGGGGGGGACTGGCGGG 667s GGTGGTGGTAGGGGGGGACTGGCGGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TCCGGGTGG 667s TCCGGGTGG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s GCGGCTC 667s GCGGCTC 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s AGAGGCG 667s AGAGGCG 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s Processing line... 667s TGGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCT 667s TGGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCT 667s Processing line... 667s GCGGTC 667s GCGGTC 667s Processing line... 667s Processing line... 667s Processing line... 667s TAGGCG 667s TAGGCG 667s Processing line... 667s Processing line... 667s TCCG 667s TCCG 667s /usr/bin/bowtie2 --rdg 14.3641351209728 --mm --score-min L,2.19987137661738,1.22568742054674 --ma 35.2106722122557 -D 27 --cp-min 3 --np 4 -i S,2.25292960624165 --cp-ival 1 -M 6 --trim5 9 --qseq -p 4 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 667s --- Summary --- 667s Read 1 reference strings 667s Checked 23 alignments, 0 edits 667s --------------- 667s PASSED 667s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 668s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 668s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (1) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 668s 139 reads; of these: 668s 139 (100.00%) were unpaired; of these: 668s 116 (83.45%) aligned 0 times 668s 11 (7.91%) aligned exactly 1 time 668s 12 (8.63%) aligned >1 times 668s 16.55% overall alignment rate 668s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 668s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 668s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 668s Flattened IUPAC characters 668s Mutating sequence Sim.pm.2 668s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 668s Finished SNPs 668s Finished ref gaps 668s Finished read gaps 668s Mutating sequence Sim.pm.1 668s Introducing 11 SNPs, 1/0 ref/read gaps, and 2 rearrangements 668s Finished SNPs 668s Finished ref gaps 668s Finished read gaps 668s Mutated reference genome to subject genome 668s SNPs introduced: 19 668s Reference gaps introduced: 1 668s Read gaps introduced: 0 668s Rearrangements introduced: 2 668s Created read sampler 668s Sampling 60 reads 668s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 668s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 668s parsing sequence Sim.pm.1... 668s parsing sequence Sim.pm.2... 668s Parsed 143 reference bases 668s *** Run 34 of 100 668s /usr/bin/bowtie2 --cp-min 2 --score-min L,2.07791018794401,1.65089611724306 -i C,2.04919180329018,5.06639445789323 --n-ceil 0.590796091462331,0.970436580240312 -R 1 --trim5 4 --cp-ival 2 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 668s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '0' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 668s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '3' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 668s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '7' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 668s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '19' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 668s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '26' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 668s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '29' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 668s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '41' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 668s Warning: skipping mate #1 of read '57' because length (1) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '57' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 668s 60 reads; of these: 668s 55 (91.67%) were paired; of these: 668s 54 (98.18%) aligned concordantly 0 times 668s 0 (0.00%) aligned concordantly exactly 1 time 668s 1 (1.82%) aligned concordantly >1 times 668s ---- 668s 54 pairs aligned concordantly 0 times; of these: 668s 1 (1.85%) aligned discordantly 1 time 668s ---- 668s 53 pairs aligned 0 times concordantly or discordantly; of these: 668s 106 mates make up the pairs; of these: 668s 91 (85.85%) aligned 0 times 668s 10 (9.43%) aligned exactly 1 time 668s 5 (4.72%) aligned >1 times 668s 5 (8.33%) were unpaired; of these: 668s 4 (80.00%) aligned 0 times 668s 1 (20.00%) aligned exactly 1 time 668s 0 (0.00%) aligned >1 times 668s 17.39% overall alignment rate 668s Read 50 alignments... 668s Read 100 alignments... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s CGG 668s CGG 668s Processing line... 668s Processing line... 668s GAGGGTGACAGAG 668s GAGGGTGACAGAG 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s AGGAGGGAGC 668s AGGAGGGAGC 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s CCGGGTGGTGTTGAGAGGGTG 668s CCGGGTGGTGTTGAGAGGGTG 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s TGAGAGGG 668s TGAGAGGG 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s AGGGGGGG 668s AGGGGGGG 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s GACAGAGGCG 668s GACAGAGGCG 668s Processing line... 668s Processing line... 668s GGGACT 668s GGGACT 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s GT 668s GT 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s CTG 668s CTG 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s AGGGGGGG 668s AGGGGGGG 668s Processing line... 668s GGTCTGCG 668s GGTCTGCG 668s Processing line... 668s Processing line... 668s Processing line... 668s GACAGAGG 668s GACAGAGG 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s CT 668s CT 668s Processing line... 668s GGTAGGGGGG 668s GGTAGGGGGG 668s Processing line... 668s Processing line... 668s Processing line... 668s CTGGTGGTG 668s CTGGTGGTG 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s GTGG 668s GTGG 668s Processing line... 668s TGAGA 668s TGAGA 668s Processing line... 668s CTCG 668s CTCG 668s Processing line... 668s Processing line... 668s GGG 668s GGG 668s Processing line... 668s Processing line... 668s Processing line... 668s --- Summary --- 668s Read 1 reference strings 668s Checked 20 alignments, 0 edits 668s --------------- 668s PASSED 668s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 668s /usr/bin/bowtie2 --cp-min 2 --score-min L,2.07791018794401,1.65089611724306 -i C,2.04919180329018,5.06639445789323 --n-ceil 0.590796091462331,0.970436580240312 -R 1 --trim5 4 --cp-ival 2 -r -p 2 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 668s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '0' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 668s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '3' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 668s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '7' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 668s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '19' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 668s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '26' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 668s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '29' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 668s Warning: skipping mate #1 of read '57' because length (1) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '57' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 668s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '41' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 668s 60 reads; of these: 668s 55 (91.67%) were paired; of these: 668s 54 (98.18%) aligned concordantly 0 times 668s 0 (0.00%) aligned concordantly exactly 1 time 668s 1 (1.82%) aligned concordantly >1 times 668s ---- 668s 54 pairs aligned concordantly 0 times; of these: 668s 1 (1.85%) aligned discordantly 1 time 668s ---- 668s 53 pairs aligned 0 times concordantly or discordantly; of these: 668s 106 mates make up the pairs; of these: 668s 91 (85.85%) aligned 0 times 668s 10 (9.43%) aligned exactly 1 time 668s 5 (4.72%) aligned >1 times 668s 5 (8.33%) were unpaired; of these: 668s 4 (80.00%) aligned 0 times 668s 1 (20.00%) aligned exactly 1 time 668s 0 (0.00%) aligned >1 times 668s 17.39% overall alignment rate 668s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 668s Flattened IUPAC characters 668s Mutating sequence Sim.pm.1 668s Introducing 6 SNPs, 0/2 ref/read gaps, and 1 rearrangements 668s Finished SNPs 668s Finished ref gaps 668s Finished read gaps 668s Mutating sequence Sim.pm.2 668s Introducing 6 SNPs, 1/0 ref/read gaps, and 1 rearrangements 668s Finished SNPs 668s Finished ref gaps 668s Finished read gaps 668s Mutated reference genome to subject genome 668s SNPs introduced: 12 668s Reference gaps introduced: 1 668s Read gaps introduced: 2 668s Rearrangements introduced: 2 668s Created read sampler 668s Sampling 42 reads 668s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 668s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 668s parsing sequence Sim.pm.1... 668s parsing sequence Sim.pm.2... 668s Parsed 143 reference bases 668s *** Run 35 of 100 668s /usr/bin/bowtie2 --trim3 0 --score-min L,2.25356354124514,5.14927252274387 -i C,2.51751955085861,9.23663885570797 --gbar 8 --local --cp-ival 2 --np 8 --cp-min 4 -q -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq 668s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 668s Warning: skipping read '3' because it was < 2 characters long 668s 42 reads; of these: 668s 42 (100.00%) were unpaired; of these: 668s 42 (100.00%) aligned 0 times 668s 0 (0.00%) aligned exactly 1 time 668s 0 (0.00%) aligned >1 times 668s 0.00% overall alignment rate 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s --- Summary --- 668s Read 1 reference strings 668s Checked 0 alignments, 0 edits 668s --------------- 668s PASSED 668s Flattened IUPAC characters 668s Mutating sequence Sim.pm.2 668s Introducing 6 SNPs, 1/1 ref/read gaps, and 1 rearrangements 668s Finished SNPs 668s Finished ref gaps 668s Finished read gaps 668s Mutating sequence Sim.pm.1 668s Introducing 10 SNPs, 1/0 ref/read gaps, and 2 rearrangements 668s Finished SNPs 668s Finished ref gaps 668s Finished read gaps 668s Mutated reference genome to subject genome 668s SNPs introduced: 16 668s Reference gaps introduced: 2 668s Read gaps introduced: 1 668s Rearrangements introduced: 3 668s Created read sampler 668s Sampling 154 reads 668s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 668s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 668s parsing sequence Sim.pm.1... 668s parsing sequence Sim.pm.2... 668s Parsed 143 reference bases 668s *** Run 36 of 100 668s /usr/bin/bowtie2 --mm --rfg 12.2203135857017 --ma 17.9856785683812 --trim3 7 --nofw --score-min L,8.97601208088967,7.68980625580695 -i L,0.347450623304259,2.81318935710988 --cp-ival 2 --cp-min 6 --trim5 4 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq 668s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (1) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (1) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_139_139_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_141_141_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_143_143_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_143_143_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_148_148_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_149_149_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_149_149_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_151_151_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_153_153_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_154_154_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_154_154_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_154_154_1/1' because it was < 2 characters long 668s Read 50 alignments... 668s 154 reads; of these: 668s 154 (100.00%) were unpaired; of these: 668s 142 (92.21%) aligned 0 times 668s 4 (2.60%) aligned exactly 1 time 668s 8 (5.19%) aligned >1 times 668s 7.79% overall alignment rate 668s Read 100 alignments... 668s Read 150 alignments... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s TAG 668s TAG 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s CGT 668s CGT 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s CGT 668s CGT 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s TG 668s TG 668s Processing line... 668s Processing line... 668s TAGGGGGGGAC 668s TAGGGGGGGAC 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s TAG 668s TAG 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s GTGA 668s GTGA 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s TGGTAGGGGGGGACTG 668s TGGTAGGGGGGGACTG 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s GGA 668s GGA 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s GA 668s GA 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s CCG 668s CCG 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s CTC 668s CTC 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s --- Summary --- 668s Read 1 reference strings 668s Checked 12 alignments, 0 edits 668s --------------- 668s PASSED 668s ALSO checking that bowtie2 and bowtie2-align match up 668s /usr/bin/bowtie2 --mm --rfg 12.2203135857017 --ma 17.9856785683812 --trim3 7 --nofw --score-min L,8.97601208088967,7.68980625580695 -i L,0.347450623304259,2.81318935710988 --cp-ival 2 --cp-min 6 --trim5 4 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 668s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (1) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (1) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_139_139_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_141_141_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_143_143_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_143_143_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_148_148_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_149_149_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_149_149_1/1' because it was < 2 characters long 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_151_151_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_153_153_1/1; setting to 0 instead 668s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_154_154_1/1; setting to 0 instead 668s Warning: skipping read 'R_1_1_1_154_154_1/1' because length (0) <= # seed mismatches (0) 668s Warning: skipping read 'R_1_1_1_154_154_1/1' because it was < 2 characters long 668s 154 reads; of these: 668s 154 (100.00%) were unpaired; of these: 668s 142 (92.21%) aligned 0 times 668s 4 (2.60%) aligned exactly 1 time 668s 8 (5.19%) aligned >1 times 668s 7.79% overall alignment rate 668s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 668s Flattened IUPAC characters 668s Mutating sequence Sim.pm.1 668s Introducing 13 SNPs, 3/1 ref/read gaps, and 0 rearrangements 668s Finished SNPs 668s Finished ref gaps 668s Finished read gaps 668s Mutating sequence Sim.pm.2 668s Introducing 7 SNPs, 1/1 ref/read gaps, and 1 rearrangements 668s Finished SNPs 668s Finished ref gaps 668s Finished read gaps 668s Mutated reference genome to subject genome 668s SNPs introduced: 20 668s Reference gaps introduced: 4 668s Read gaps introduced: 2 668s Rearrangements introduced: 1 668s Created read sampler 668s Sampling 68 reads 668s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 668s *** Run 37 of 100 668s /usr/bin/bowtie2 --rfg 38.8702481658995 --mp 3.46422517274466,2.29863002727905 --local --cp-ival 1 --trim5 7 --rdg 48.1741038732225,3.2717513572885 --mm --score-min L,7.10757238284855,8.80396348672775 -R 4 -k 5 --gbar 1 --cp-min 5 --np 3 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 668s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 668s parsing sequence Sim.pm.1... 668s parsing sequence Sim.pm.2... 668s Parsed 143 reference bases 668s Warning: skipping mate #1 of read '0' because length (1) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '0' because it was < 2 characters long 668s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '4' because it was < 2 characters long 668s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '7' because it was < 2 characters long 668s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 668s Warning: skipping mate #2 of read '14' because it was < 2 characters long 668s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '17' because it was < 2 characters long 668s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '25' because it was < 2 characters long 668s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 668s Warning: skipping mate #2 of read '32' because it was < 2 characters long 668s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '37' because it was < 2 characters long 668s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 668s Warning: skipping read '43' because it was < 2 characters long 668s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '46' because it was < 2 characters long 668s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '48' because it was < 2 characters long 668s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 668s Warning: skipping mate #1 of read '51' because it was < 2 characters long 668s Read 50 alignments... 668s Read 100 alignments... 668s 68 reads; of these: 668s 57 (83.82%) were paired; of these: 668s 57 (100.00%) aligned concordantly 0 times 668s 0 (0.00%) aligned concordantly exactly 1 time 668s 0 (0.00%) aligned concordantly >1 times 668s ---- 668s 57 pairs aligned concordantly 0 times; of these: 668s 0 (0.00%) aligned discordantly 1 time 668s ---- 668s 57 pairs aligned 0 times concordantly or discordantly; of these: 668s 114 mates make up the pairs; of these: 668s 114 (100.00%) aligned 0 times 668s 0 (0.00%) aligned exactly 1 time 668s 0 (0.00%) aligned >1 times 668s 11 (16.18%) were unpaired; of these: 668s 11 (100.00%) aligned 0 times 668s 0 (0.00%) aligned exactly 1 time 668s 0 (0.00%) aligned >1 times 668s 0.00% overall alignment rate 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s *** Run 38 of 100 668s /usr/bin/bowtie2 --trim5 2 --cp-min 2 --np 4 --cp-ival 1 --gbar 6 --trim3 2 --score-min L,2.84114996367029,5.16218766979219 -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s Processing line... 668s --- Summary --- 668s Read 1 reference strings 668s Checked 0 alignments, 0 edits 668s --------------- 668s PASSED 668s Flattened IUPAC characters 668s Mutating sequence Sim.pm.2 668s Introducing 13 SNPs, 1/1 ref/read gaps, and 2 rearrangements 668s Finished SNPs 668s Finished ref gaps 668s Finished read gaps 668s Mutating sequence Sim.pm.1 668s Introducing 7 SNPs, 3/0 ref/read gaps, and 0 rearrangements 668s Finished SNPs 668s Finished ref gaps 668s Finished read gaps 668s Mutated reference genome to subject genome 668s SNPs introduced: 20 668s Reference gaps introduced: 4 668s Read gaps introduced: 1 668s Rearrangements introduced: 2 668s Created read sampler 668s Sampling 42 reads 668s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 668s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 668s parsing sequence Sim.pm.1... 668s parsing sequence Sim.pm.2... 668s Parsed 143 reference bases 669s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 669s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 669s Warning: skipping read '2' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 669s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 669s Warning: skipping read '22' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 669s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 669s Warning: skipping read '30' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 669s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 669s Warning: skipping read '31' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 669s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 669s Warning: skipping read '39' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 669s 42 reads; of these: 669s 42 (100.00%) were unpaired; of these: 669s 33 (78.57%) aligned 0 times 669s 4 (9.52%) aligned exactly 1 time 669s 5 (11.90%) aligned >1 times 669s 21.43% overall alignment rate 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s CGGTC 669s CGGTC 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s GG 669s GG 669s Processing line... 669s Processing line... 669s GGT 669s GGT 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s /usr/bin/bowtie2 --trim5 2 --cp-min 2 --np 4 --cp-ival 1 --gbar 6 --trim3 2 --score-min L,2.84114996367029,5.16218766979219 -r -p 3 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 669s Processing line... 669s Processing line... 669s TGGTAGGGGGGGACTGGCGGGAAGAC 669s TGGTAGGGGGGGACTGGCGGGAAGAC 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s GT 669s GT 669s Processing line... 669s Processing line... 669s Processing line... 669s GGTGGTGGTAGGGGGGGA 669s GGTGGTGGTAGGGGGGGA 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s GGGGGACTGGCGGG 669s GGGGGACTGGCGGG 669s Processing line... 669s Processing line... 669s Processing line... 669s GG 669s GG 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s GGTGGTAGGGGGGGACT 669s GGTGGTAGGGGGGGACT 669s Processing line... 669s --- Summary --- 669s Read 1 reference strings 669s Checked 9 alignments, 0 edits 669s --------------- 669s PASSED 669s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 669s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 669s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 669s Warning: skipping read '2' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 669s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 669s Warning: skipping read '22' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 669s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 669s Warning: skipping read '39' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 669s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 669s Warning: skipping read '30' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 669s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 669s Warning: skipping read '31' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 669s 42 reads; of these: 669s 42 (100.00%) were unpaired; of these: 669s 33 (78.57%) aligned 0 times 669s 4 (9.52%) aligned exactly 1 time 669s 5 (11.90%) aligned >1 times 669s 21.43% overall alignment rate 669s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 669s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 669s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 669s *** Run 39 of 100 669s /usr/bin/bowtie2 --cp-ival 1 -a --n-ceil 1.16674027483581,0.907983524342347 --rfg 20.7498725083373 --nofw -N 0 -L29 --cp-min 3 --np 1 --rdg 30.2287549541538,8.16231840792907 --mm --score-min L,4.96120242714053,4.22391061486323 --gbar 3 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 669s Flattened IUPAC characters 669s Mutating sequence Sim.pm.1 669s Introducing 0 SNPs, 1/0 ref/read gaps, and 3 rearrangements 669s Finished SNPs 669s Finished ref gaps 669s Finished read gaps 669s Mutating sequence Sim.pm.2 669s Introducing 7 SNPs, 3/0 ref/read gaps, and 0 rearrangements 669s Finished SNPs 669s Finished ref gaps 669s Finished read gaps 669s Mutated reference genome to subject genome 669s SNPs introduced: 7 669s Reference gaps introduced: 4 669s Read gaps introduced: 0 669s Rearrangements introduced: 3 669s Created read sampler 669s Sampling 6 reads 669s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 669s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 669s parsing sequence Sim.pm.1... 669s parsing sequence Sim.pm.2... 669s Parsed 143 reference bases 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 669s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read '3' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 669s 6 reads; of these: 669s 6 (100.00%) were paired; of these: 669s 6 (100.00%) aligned concordantly 0 times 669s 0 (0.00%) aligned concordantly exactly 1 time 669s 0 (0.00%) aligned concordantly >1 times 669s ---- 669s 6 pairs aligned concordantly 0 times; of these: 669s 0 (0.00%) aligned discordantly 1 time 669s ---- 669s 6 pairs aligned 0 times concordantly or discordantly; of these: 669s 12 mates make up the pairs; of these: 669s 10 (83.33%) aligned 0 times 669s 1 (8.33%) aligned exactly 1 time 669s 1 (8.33%) aligned >1 times 669s 16.67% overall alignment rate 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s GC 669s GC 669s Processing line... 669s GC 669s GC 669s Processing line... 669s GC 669s GC 669s Processing line... 669s GC 669s GC 669s Processing line... 669s GC 669s GC 669s Processing line... 669s GC 669s GC 669s Processing line... 669s GC 669s GC 669s Processing line... 669s GC 669s GC 669s Processing line... 669s GC 669s GC 669s Processing line... 669s GC 669s GC 669s Processing line... 669s Processing line... 669s GGGTGGTGTTGAGAGGG 669s GGGTGGTGTTGAGAGGG 669s Processing line... 669s /usr/bin/bowtie2 --cp-ival 1 -a --n-ceil 1.16674027483581,0.907983524342347 --rfg 20.7498725083373 --nofw -N 0 -L29 --cp-min 3 --np 1 --rdg 30.2287549541538,8.16231840792907 --mm --score-min L,4.96120242714053,4.22391061486323 --gbar 3 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s --- Summary --- 669s Read 1 reference strings 669s Checked 11 alignments, 0 edits 669s --------------- 669s PASSED 669s ALSO checking that bowtie2 and bowtie2-align match up 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 669s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read '3' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 669s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 669s 6 reads; of these: 669s 6 (100.00%) were paired; of these: 669s 6 (100.00%) aligned concordantly 0 times 669s 0 (0.00%) aligned concordantly exactly 1 time 669s 0 (0.00%) aligned concordantly >1 times 669s ---- 669s 6 pairs aligned concordantly 0 times; of these: 669s 0 (0.00%) aligned discordantly 1 time 669s ---- 669s 6 pairs aligned 0 times concordantly or discordantly; of these: 669s 12 mates make up the pairs; of these: 669s 10 (83.33%) aligned 0 times 669s 1 (8.33%) aligned exactly 1 time 669s 1 (8.33%) aligned >1 times 669s 16.67% overall alignment rate 669s /usr/bin/bowtie2 --cp-ival 1 -a --n-ceil 1.16674027483581,0.907983524342347 --rfg 20.7498725083373 --nofw -N 0 -L29 --cp-min 3 --np 1 --rdg 30.2287549541538,8.16231840792907 --mm --score-min L,4.96120242714053,4.22391061486323 --gbar 3 -r -p 3 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 669s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 669s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read '3' because it was < 2 characters long 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 669s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 669s 6 reads; of these: 669s 6 (100.00%) were paired; of these: 669s 6 (100.00%) aligned concordantly 0 times 669s 0 (0.00%) aligned concordantly exactly 1 time 669s 0 (0.00%) aligned concordantly >1 times 669s ---- 669s 6 pairs aligned concordantly 0 times; of these: 669s 0 (0.00%) aligned discordantly 1 time 669s ---- 669s 6 pairs aligned 0 times concordantly or discordantly; of these: 669s 12 mates make up the pairs; of these: 669s 10 (83.33%) aligned 0 times 669s 1 (8.33%) aligned exactly 1 time 669s 1 (8.33%) aligned >1 times 669s 16.67% overall alignment rate 669s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 669s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 669s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 669s Flattened IUPAC characters 669s Mutating sequence Sim.pm.1 669s Introducing 3 SNPs, 2/2 ref/read gaps, and 2 rearrangements 669s Finished SNPs 669s Finished ref gaps 669s Finished read gaps 669s Mutating sequence Sim.pm.2 669s Introducing 11 SNPs, 1/1 ref/read gaps, and 0 rearrangements 669s Finished SNPs 669s Finished ref gaps 669s Finished read gaps 669s Mutated reference genome to subject genome 669s SNPs introduced: 14 669s Reference gaps introduced: 3 669s Read gaps introduced: 3 669s Rearrangements introduced: 2 669s Created read sampler 669s Sampling 170 reads 669s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 669s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 669s parsing sequence Sim.pm.1... 669s *** Run 40 of 100 669s /usr/bin/bowtie2 --rfg 26.5548023922174,19.4051914538449 --score-min L,4.55589499708781,3.09707911603699 --local --cp-ival 2 -a --cp-min 6 --trim5 0 --n-ceil 0.290312578285378,0.538443422069629 --norc --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 669s parsing sequence Sim.pm.2... 669s Parsed 143 reference bases 669s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 669s Read 50 alignments... 669s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_151_151_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_152_152_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_152_152_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_153_153_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_153_153_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 669s Read 100 alignments... 669s Warning: skipping mate #2 of read 'R_1_1_1_163_163_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_163_163_1/1' because it was < 2 characters long 669s Read 150 alignments... 669s 170 reads; of these: 669s 170 (100.00%) were paired; of these: 669s 170 (100.00%) aligned concordantly 0 times 669s 0 (0.00%) aligned concordantly exactly 1 time 669s 0 (0.00%) aligned concordantly >1 times 669s ---- 669s 170 pairs aligned concordantly 0 times; of these: 669s 0 (0.00%) aligned discordantly 1 time 669s ---- 669s 170 pairs aligned 0 times concordantly or discordantly; of these: 669s 340 mates make up the pairs; of these: 669s 340 (100.00%) aligned 0 times 669s 0 (0.00%) aligned exactly 1 time 669s 0 (0.00%) aligned >1 times 669s 0.00% overall alignment rate 669s Read 200 alignments... 669s Read 250 alignments... 669s Read 300 alignments... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing 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Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s Processing line... 669s --- Summary --- 669s Read 1 reference strings 669s Checked 0 alignments, 0 edits 669s --------------- 669s PASSED 669s ALSO checking that bowtie2 and bowtie2-align match up 669s /usr/bin/bowtie2 --rfg 26.5548023922174,19.4051914538449 --score-min L,4.55589499708781,3.09707911603699 --local --cp-ival 2 -a --cp-min 6 --trim5 0 --n-ceil 0.290312578285378,0.538443422069629 --norc --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 669s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_151_151_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_152_152_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_152_152_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_153_153_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_153_153_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_163_163_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_163_163_1/1' because it was < 2 characters long 669s 170 reads; of these: 669s 170 (100.00%) were paired; of these: 669s 170 (100.00%) aligned concordantly 0 times 669s 0 (0.00%) aligned concordantly exactly 1 time 669s 0 (0.00%) aligned concordantly >1 times 669s ---- 669s 170 pairs aligned concordantly 0 times; of these: 669s 0 (0.00%) aligned discordantly 1 time 669s ---- 669s 170 pairs aligned 0 times concordantly or discordantly; of these: 669s 340 mates make up the pairs; of these: 669s 340 (100.00%) aligned 0 times 669s 0 (0.00%) aligned exactly 1 time 669s 0 (0.00%) aligned >1 times 669s 0.00% overall alignment rate 669s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 669s /usr/bin/bowtie2 --rfg 26.5548023922174,19.4051914538449 --score-min L,4.55589499708781,3.09707911603699 --local --cp-ival 2 -a --cp-min 6 --trim5 0 --n-ceil 0.290312578285378,0.538443422069629 --norc --qseq -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 669s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 669s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_151_151_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_152_152_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_152_152_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_153_153_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_153_153_1/1' because it was < 2 characters long 669s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 669s Warning: skipping mate #2 of read 'R_1_1_1_163_163_1/1' because length (1) <= # seed mismatches (0) 669s Warning: skipping mate #2 of read 'R_1_1_1_163_163_1/1' because it was < 2 characters long 670s 170 reads; of these: 670s 170 (100.00%) were paired; of these: 670s 170 (100.00%) aligned concordantly 0 times 670s 0 (0.00%) aligned concordantly exactly 1 time 670s 0 (0.00%) aligned concordantly >1 times 670s ---- 670s 170 pairs aligned concordantly 0 times; of these: 670s 0 (0.00%) aligned discordantly 1 time 670s ---- 670s 170 pairs aligned 0 times concordantly or discordantly; of these: 670s 340 mates make up the pairs; of these: 670s 340 (100.00%) aligned 0 times 670s 0 (0.00%) aligned exactly 1 time 670s 0 (0.00%) aligned >1 times 670s 0.00% overall alignment rate 670s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 670s *** Run 41 of 100 670s /usr/bin/bowtie2 --norc --trim5 1 --cp-ival 3 --trim3 0 --mp 3.85961759466096,2.73930821420681 --rfg 42.0762129884577,1.98792291757346 --np 2 --cp-min 3 --score-min L,9.71109780131062,2.06159688310499 --ma 4.40866270183415 -D 35 --mm -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 670s Flattened IUPAC characters 670s Mutating sequence Sim.pm.1 670s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 670s Finished SNPs 670s Finished ref gaps 670s Finished read gaps 670s Mutating sequence Sim.pm.2 670s Introducing 6 SNPs, 2/0 ref/read gaps, and 0 rearrangements 670s Finished SNPs 670s Finished ref gaps 670s Finished read gaps 670s Mutated reference genome to subject genome 670s SNPs introduced: 16 670s Reference gaps introduced: 2 670s Read gaps introduced: 0 670s Rearrangements introduced: 0 670s Created read sampler 670s Sampling 123 reads 670s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 670s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 670s parsing sequence Sim.pm.1... 670s parsing sequence Sim.pm.2... 670s Parsed 143 reference bases 670s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 670s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 670s Warning: skipping mate #2 of read '7' because it was < 2 characters long 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 670s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '27' because it was < 2 characters long 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 670s Read 50 alignments... 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 670s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '52' because it was < 2 characters long 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 670s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 670s Warning: skipping mate #2 of read '61' because it was < 2 characters long 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 670s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '83' because it was < 2 characters long 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 670s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '103' because it was < 2 characters long 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 670s Read 100 alignments... 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 670s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 670s Read 150 alignments... 670s 123 reads; of these: 670s 121 (98.37%) were paired; of these: 670s 121 (100.00%) aligned concordantly 0 times 670s 0 (0.00%) aligned concordantly exactly 1 time 670s 0 (0.00%) aligned concordantly >1 times 670s ---- 670s 121 pairs aligned concordantly 0 times; of these: 670s 0 (0.00%) aligned discordantly 1 time 670s ---- 670s 121 pairs aligned 0 times concordantly or discordantly; of these: 670s 242 mates make up the pairs; of these: 670s 210 (86.78%) aligned 0 times 670s 16 (6.61%) aligned exactly 1 time 670s 16 (6.61%) aligned >1 times 670s 2 (1.63%) were unpaired; of these: 670s 1 (50.00%) aligned 0 times 670s 1 (50.00%) aligned exactly 1 time 670s 0 (0.00%) aligned >1 times 670s 13.52% overall alignment rate 670s Read 200 alignments... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s TC 670s TC 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s TC 670s TC 670s Processing line... 670s Processing line... 670s TGG 670s TGG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GTGGTAGGGGGGGACTGGCGGGAAG 670s GTGGTAGGGGGGGACTGGCGGGAAG 670s Processing line... 670s Processing line... 670s AGGG 670s AGGG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s TC 670s TC 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GTGTTGAGAGGGTGACAGAGG 670s GTGTTGAGAGGGTGACAGAGG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GTGG 670s GTGG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s CAGAGGCGTGG 670s CAGAGGCGTGG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s CC 670s CC 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GGAGGGAGCTG 670s GGAGGGAGCTG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GTAG 670s GTAG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s CTGCGCCCAGCTTA 670s CTGCGCCCAGCTTA 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s TCGGTCTGCGCCCAGCTTA 670s TCGGTCTGCGCCCAGCTTA 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s TCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGC 670s TCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGC 670s Processing line... 670s Processing line... 670s CTTAG 670s CTTAG 670s Processing line... 670s CAGAGGCGTGG 670s CAGAGGCGTGG 670s Processing line... 670s Processing line... 670s TGGTG 670s TGGTG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GTCTGCGCCCA 670s GTCTGCGCCCA 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s TCGGT 670s TCGGT 670s Processing line... 670s Processing line... 670s GAGAGGGTG 670s GAGAGGGTG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GTGGTG 670s GTGGTG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GTGGT 670s GTGGT 670s Processing line... 670s Processing line... 670s GTGACA 670s GTGACA 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GCGT 670s GCGT 670s Processing line... 670s Processing line... 670s CC 670s CC 670s Processing line... 670s Processing line... 670s GTGGTAGGGGGGGACTG 670s GTGGTAGGGGGGGACTG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GGGGG 670s GGGGG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s CC 670s CC 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GC 670s GC 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GGGG 670s GGGG 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s TGC 670s TGC 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s GTGGTGTTGAGAGGGTGAC 670s GTGGTGTTGAGAGGGTGAC 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s --- Summary --- 670s Read 1 reference strings 670s Checked 33 alignments, 0 edits 670s --------------- 670s PASSED 670s Flattened IUPAC characters 670s Mutating sequence Sim.pm.2 670s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 670s Finished SNPs 670s Finished ref gaps 670s Finished read gaps 670s Mutating sequence Sim.pm.1 670s *** Run 42 of 100 670s /usr/bin/bowtie2 --np 2 --cp-min 3 -D 19 --score-min L,6.67337065387355,4.51215056354776 --mm --n-ceil 0.680874122946663,0.933412918280856 --trim5 4 --norc -M 9 --cp-ival 2 --local --mp 2.8291062579835,1.01040012337454 --rfg 26.7183196442468,7.51570913048241 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 670s Introducing 3 SNPs, 0/2 ref/read gaps, and 0 rearrangements 670s Finished SNPs 670s Finished ref gaps 670s Finished read gaps 670s Mutated reference genome to subject genome 670s SNPs introduced: 3 670s Reference gaps introduced: 1 670s Read gaps introduced: 2 670s Rearrangements introduced: 1 670s Created read sampler 670s Sampling 136 reads 670s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 670s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 670s parsing sequence Sim.pm.1... 670s parsing sequence Sim.pm.2... 670s Parsed 143 reference bases 670s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 670s Warning: skipping mate #1 of read '6' because length (1) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '6' because it was < 2 characters long 670s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '15' because it was < 2 characters long 670s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '21' because it was < 2 characters long 670s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '22' because it was < 2 characters long 670s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '30' because it was < 2 characters long 670s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '43' because it was < 2 characters long 670s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '54' because it was < 2 characters long 670s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '56' because it was < 2 characters long 670s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '61' because it was < 2 characters long 670s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '70' because it was < 2 characters long 670s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '75' because it was < 2 characters long 670s Read 50 alignments... 670s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '96' because it was < 2 characters long 670s Warning: skipping mate #1 of read '104' because length (1) <= # seed mismatches (0) 670s Warning: skipping mate #1 of read '104' because it was < 2 characters long 670s Read 100 alignments... 670s *** Run 43 of 100 670s /usr/bin/bowtie2 --trim5 7 -M 6 --cp-min 3 --np 3 --cp-ival 4 --local --score-min L,7.31804693771246,4.44042186692164 --rfg 11.5999928186645,8.52660608606484 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 670s Read 150 alignments... 670s 136 reads; of these: 670s 123 (90.44%) were paired; of these: 670s 123 (100.00%) aligned concordantly 0 times 670s 0 (0.00%) aligned concordantly exactly 1 time 670s 0 (0.00%) aligned concordantly >1 times 670s ---- 670s 123 pairs aligned concordantly 0 times; of these: 670s 0 (0.00%) aligned discordantly 1 time 670s ---- 670s 123 pairs aligned 0 times concordantly or discordantly; of these: 670s 246 mates make up the pairs; of these: 670s 246 (100.00%) aligned 0 times 670s 0 (0.00%) aligned exactly 1 time 670s 0 (0.00%) aligned >1 times 670s 13 (9.56%) were unpaired; of these: 670s 13 (100.00%) aligned 0 times 670s 0 (0.00%) aligned exactly 1 time 670s 0 (0.00%) aligned >1 times 670s 0.00% overall alignment rate 670s Read 200 alignments... 670s Read 250 alignments... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s --- Summary --- 670s Read 1 reference strings 670s Checked 0 alignments, 0 edits 670s --------------- 670s PASSED 670s Flattened IUPAC characters 670s Mutating sequence Sim.pm.2 670s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 670s Finished SNPs 670s Finished ref gaps 670s Finished read gaps 670s Mutating sequence Sim.pm.1 670s Introducing 11 SNPs, 0/0 ref/read gaps, and 1 rearrangements 670s Finished SNPs 670s Finished ref gaps 670s Finished read gaps 670s Mutated reference genome to subject genome 670s SNPs introduced: 16 670s Reference gaps introduced: 0 670s Read gaps introduced: 0 670s Rearrangements introduced: 2 670s Created read sampler 670s Sampling 188 reads 670s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 670s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 670s parsing sequence Sim.pm.1... 670s parsing sequence Sim.pm.2... 670s Parsed 143 reference bases 670s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 670s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '11' because it was < 2 characters long 670s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '13' because it was < 2 characters long 670s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '23' because it was < 2 characters long 670s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '26' because it was < 2 characters long 670s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '27' because it was < 2 characters long 670s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '46' because it was < 2 characters long 670s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '49' because it was < 2 characters long 670s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '53' because it was < 2 characters long 670s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '59' because it was < 2 characters long 670s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '63' because it was < 2 characters long 670s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '64' because it was < 2 characters long 670s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '68' because it was < 2 characters long 670s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '70' because it was < 2 characters long 670s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '75' because it was < 2 characters long 670s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '77' because it was < 2 characters long 670s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '80' because it was < 2 characters long 670s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '83' because it was < 2 characters long 670s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '85' because it was < 2 characters long 670s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '91' because it was < 2 characters long 670s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '96' because it was < 2 characters long 670s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '100' because it was < 2 characters long 670s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '101' because it was < 2 characters long 670s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '103' because it was < 2 characters long 670s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '106' because it was < 2 characters long 670s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '111' because it was < 2 characters long 670s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '119' because it was < 2 characters long 670s Warning: skipping read '125' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '125' because it was < 2 characters long 670s Warning: skipping read '130' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '130' because it was < 2 characters long 670s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '131' because it was < 2 characters long 670s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '136' because it was < 2 characters long 670s Warning: skipping read '139' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '139' because it was < 2 characters long 670s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '143' because it was < 2 characters long 670s Warning: skipping read '164' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '164' because it was < 2 characters long 670s Warning: skipping read '170' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '170' because it was < 2 characters long 670s Warning: skipping read '175' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '175' because it was < 2 characters long 670s Warning: skipping read '177' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '177' because it was < 2 characters long 670s Warning: skipping read '179' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '179' because it was < 2 characters long 670s Warning: skipping read '182' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '182' because it was < 2 characters long 670s Warning: skipping read '183' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '183' because it was < 2 characters long 670s Warning: skipping read '186' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '186' because it was < 2 characters long 670s Read 50 alignments... 670s 188 reads; of these: 670s 188 (100.00%) were unpaired; of these: 670s 188 (100.00%) aligned 0 times 670s 0 (0.00%) aligned exactly 1 time 670s 0 (0.00%) aligned >1 times 670s 0.00% overall alignment rate 670s Read 100 alignments... 670s Read 150 alignments... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s --- Summary --- 670s Read 1 reference strings 670s Checked 0 alignments, 0 edits 670s --------------- 670s PASSED 670s Flattened IUPAC characters 670s Mutating sequence Sim.pm.2 670s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 670s Finished SNPs 670s Finished ref gaps 670s Finished read gaps 670s Mutating sequence Sim.pm.1 670s Introducing 1 SNPs, 0/4 ref/read gaps, and 2 rearrangements 670s Finished SNPs 670s Finished ref gaps 670s Finished read gaps 670s Mutated reference genome to subject genome 670s SNPs introduced: 6 670s Reference gaps introduced: 1 670s Read gaps introduced: 4 670s Rearrangements introduced: 2 670s Created read sampler 670s Sampling 155 reads 670s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 670s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 670s parsing sequence Sim.pm.1... 670s parsing sequence Sim.pm.2... 670s Parsed 143 reference bases 670s *** Run 44 of 100 670s /usr/bin/bowtie2 --local --cp-ival 1 --cp-min 3 --trim5 0 --rfg 48.2579829091805 --mm --trim3 6 --score-min L,7.29297515559145,9.36219633640102 -N 1 -L28 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 670s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '14' because it was < 2 characters long 670s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '21' because it was < 2 characters long 670s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '43' because it was < 2 characters long 670s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '57' because it was < 2 characters long 670s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '63' because it was < 2 characters long 670s Warning: skipping read '72' because length (1) <= # seed mismatches (1) 670s Warning: skipping read '72' because it was < 2 characters long 670s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '79' because it was < 2 characters long 670s Warning: skipping mate #1 of read '94' because length (1) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '94' because it was < 2 characters long 670s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '99' because it was < 2 characters long 670s Warning: skipping mate #2 of read '99' because it was < 2 characters long 670s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '103' because it was < 2 characters long 670s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '105' because it was < 2 characters long 670s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '112' because it was < 2 characters long 670s Warning: skipping mate #2 of read '122' because length (1) <= # seed mismatches (1) 670s Warning: skipping mate #2 of read '122' because it was < 2 characters long 670s Warning: skipping mate #1 of read '130' because length (0) <= # seed mismatches (1) 670s Read 50 alignments... 670s Warning: skipping mate #1 of read '130' because it was < 2 characters long 670s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '133' because it was < 2 characters long 670s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '136' because it was < 2 characters long 670s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '144' because it was < 2 characters long 670s Warning: skipping mate #1 of read '147' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '147' because it was < 2 characters long 670s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '151' because it was < 2 characters long 670s 155 reads; of these: 670s 128 (82.58%) were paired; of these: 670s 128 (100.00%) aligned concordantly 0 times 670s 0 (0.00%) aligned concordantly exactly 1 time 670s 0 (0.00%) aligned concordantly >1 times 670s ---- 670s 128 pairs aligned concordantly 0 times; of these: 670s 0 (0.00%) aligned discordantly 1 time 670s ---- 670s 128 pairs aligned 0 times concordantly or discordantly; of these: 670s 256 mates make up the pairs; of these: 670s 256 (100.00%) aligned 0 times 670s 0 (0.00%) aligned exactly 1 time 670s 0 (0.00%) aligned >1 times 670s 27 (17.42%) were unpaired; of these: 670s 27 (100.00%) aligned 0 times 670s 0 (0.00%) aligned exactly 1 time 670s 0 (0.00%) aligned >1 times 670s 0.00% overall alignment rate 670s Read 100 alignments... 670s Read 150 alignments... 670s Read 200 alignments... 670s Read 250 alignments... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing 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line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s 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line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s /usr/bin/bowtie2 --local --cp-ival 1 --cp-min 3 --trim5 0 --rfg 48.2579829091805 --mm --trim3 6 --score-min L,7.29297515559145,9.36219633640102 -N 1 -L28 -r -p 4 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s --- Summary --- 670s Read 1 reference strings 670s Checked 0 alignments, 0 edits 670s --------------- 670s PASSED 670s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 670s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '14' because it was < 2 characters long 670s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '21' because it was < 2 characters long 670s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '43' because it was < 2 characters long 670s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '57' because it was < 2 characters long 670s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '63' because it was < 2 characters long 670s Warning: skipping read '72' because length (1) <= # seed mismatches (1) 670s Warning: skipping read '72' because it was < 2 characters long 670s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '79' because it was < 2 characters long 670s Warning: skipping mate #1 of read '94' because length (1) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '94' because it was < 2 characters long 670s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '99' because it was < 2 characters long 670s Warning: skipping mate #2 of read '99' because it was < 2 characters long 670s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '103' because it was < 2 characters long 670s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '105' because it was < 2 characters long 670s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '112' because it was < 2 characters long 670s Warning: skipping mate #2 of read '122' because length (1) <= # seed mismatches (1) 670s Warning: skipping mate #2 of read '122' because it was < 2 characters long 670s Warning: skipping mate #1 of read '130' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '130' because it was < 2 characters long 670s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '133' because it was < 2 characters long 670s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '136' because it was < 2 characters long 670s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '144' because it was < 2 characters long 670s Warning: skipping mate #1 of read '147' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '147' because it was < 2 characters long 670s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (1) 670s Warning: skipping mate #1 of read '151' because it was < 2 characters long 670s 155 reads; of these: 670s 128 (82.58%) were paired; of these: 670s 128 (100.00%) aligned concordantly 0 times 670s 0 (0.00%) aligned concordantly exactly 1 time 670s 0 (0.00%) aligned concordantly >1 times 670s ---- 670s 128 pairs aligned concordantly 0 times; of these: 670s 0 (0.00%) aligned discordantly 1 time 670s ---- 670s 128 pairs aligned 0 times concordantly or discordantly; of these: 670s 256 mates make up the pairs; of these: 670s 256 (100.00%) aligned 0 times 670s 0 (0.00%) aligned exactly 1 time 670s 0 (0.00%) aligned >1 times 670s 27 (17.42%) were unpaired; of these: 670s 27 (100.00%) aligned 0 times 670s 0 (0.00%) aligned exactly 1 time 670s 0 (0.00%) aligned >1 times 670s 0.00% overall alignment rate 670s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 670s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 670s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 670s Flattened IUPAC characters 670s Mutating sequence Sim.pm.2 670s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 670s Finished SNPs 670s Finished ref gaps 670s Finished read gaps 670s Mutating sequence Sim.pm.1 670s Introducing 12 SNPs, 0/0 ref/read gaps, and 1 rearrangements 670s Finished SNPs 670s Finished ref gaps 670s Finished read gaps 670s Mutated reference genome to subject genome 670s SNPs introduced: 17 670s Reference gaps introduced: 0 670s Read gaps introduced: 0 670s Rearrangements introduced: 1 670s Created read sampler 670s Sampling 126 reads 670s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 670s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 670s parsing sequence Sim.pm.1... 670s parsing sequence Sim.pm.2... 670s Parsed 143 reference bases 670s *** Run 45 of 100 670s /usr/bin/bowtie2 --rdg 48.5106309649552,13.5449231869161 -R 4 --score-min L,1.90394273299497,2.14813265651058 --np 4 --cp-min 3 --mp 4.24521742614148,4.22854395090893 --nofw --cp-ival 1 --local --trim5 2 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 670s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '29' because it was < 2 characters long 670s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '32' because it was < 2 characters long 670s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '40' because it was < 2 characters long 670s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '56' because it was < 2 characters long 670s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '61' because it was < 2 characters long 670s Warning: skipping read '80' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '80' because it was < 2 characters long 670s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '87' because it was < 2 characters long 670s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '120' because it was < 2 characters long 670s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '126' because it was < 2 characters long 670s 126 reads; of these: 670s 126 (100.00%) were unpaired; of these: 670s 126 (100.00%) aligned 0 times 670s 0 (0.00%) aligned exactly 1 time 670s 0 (0.00%) aligned >1 times 670s 0.00% overall alignment rate 670s Read 50 alignments... 670s Read 100 alignments... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s Processing line... 670s --- Summary --- 670s Read 1 reference strings 670s Checked 0 alignments, 0 edits 670s --------------- 670s PASSED 670s ALSO checking that bowtie2 and bowtie2-align match up 670s /usr/bin/bowtie2 --rdg 48.5106309649552,13.5449231869161 -R 4 --score-min L,1.90394273299497,2.14813265651058 --np 4 --cp-min 3 --mp 4.24521742614148,4.22854395090893 --nofw --cp-ival 1 --local --trim5 2 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 670s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '29' because it was < 2 characters long 670s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '32' because it was < 2 characters long 670s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '40' because it was < 2 characters long 670s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '56' because it was < 2 characters long 670s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '61' because it was < 2 characters long 670s Warning: skipping read '80' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '80' because it was < 2 characters long 670s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '87' because it was < 2 characters long 670s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '120' because it was < 2 characters long 670s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '126' because it was < 2 characters long 670s 126 reads; of these: 670s 126 (100.00%) were unpaired; of these: 670s 126 (100.00%) aligned 0 times 670s 0 (0.00%) aligned exactly 1 time 670s 0 (0.00%) aligned >1 times 670s 0.00% overall alignment rate 670s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 670s /usr/bin/bowtie2 --rdg 48.5106309649552,13.5449231869161 -R 4 --score-min L,1.90394273299497,2.14813265651058 --np 4 --cp-min 3 --mp 4.24521742614148,4.22854395090893 --nofw --cp-ival 1 --local --trim5 2 -f -p 4 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 670s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 670s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '29' because it was < 2 characters long 670s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '32' because it was < 2 characters long 670s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '40' because it was < 2 characters long 670s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '56' because it was < 2 characters long 670s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '61' because it was < 2 characters long 670s Warning: skipping read '80' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '80' because it was < 2 characters long 670s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 670s Warning: skipping read '87' because it was < 2 characters long 670s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '120' because it was < 2 characters long 670s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 670s Warning: skipping read '126' because it was < 2 characters long 670s 126 reads; of these: 670s 126 (100.00%) were unpaired; of these: 670s 126 (100.00%) aligned 0 times 670s 0 (0.00%) aligned exactly 1 time 670s 0 (0.00%) aligned >1 times 670s 0.00% overall alignment rate 670s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 670s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 670s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 670s Flattened IUPAC characters 670s Mutating sequence Sim.pm.2 670s Introducing 4 SNPs, 0/1 ref/read gaps, and 2 rearrangements 670s Finished SNPs 670s Finished ref gaps 670s Finished read gaps 670s Mutating sequence Sim.pm.1 670s Introducing 14 SNPs, 0/2 ref/read gaps, and 0 rearrangements 670s Finished SNPs 670s Finished ref gaps 670s Finished read gaps 670s Mutated reference genome to subject genome 670s SNPs introduced: 18 670s Reference gaps introduced: 0 670s Read gaps introduced: 3 670s Rearrangements introduced: 2 670s Created read sampler 670s Sampling 79 reads 670s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 670s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 670s *** Run 46 of 100 670s /usr/bin/bowtie2 --cp-min 5 --np 2 --cp-ival 1 --nofw --ma 12.0873719078613 --trim3 5 --score-min L,1.09241216250464,5.20806074640023 --mp 6.27920316333523,4.47329852554499 -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw 670s parsing sequence Sim.pm.1... 670s parsing sequence Sim.pm.2... 670s Parsed 143 reference bases 671s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 671s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 671s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '4' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 671s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '9' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 671s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '20' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 671s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '22' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 671s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '23' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 671s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '24' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 671s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '26' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 671s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 671s Warning: skipping read '47' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 671s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '48' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 671s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '50' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 671s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '60' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 671s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '65' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 671s 79 reads; of these: 671s 79 (100.00%) were unpaired; of these: 671s 68 (86.08%) aligned 0 times 671s 7 (8.86%) aligned exactly 1 time 671s 4 (5.06%) aligned >1 times 671s 13.92% overall alignment rate 671s Read 50 alignments... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s CGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGCTGG 671s CGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGCTGG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s AGAG 671s AGAG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s CGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGCTGG 671s CGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGCTGG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s /usr/bin/bowtie2 --cp-min 5 --np 2 --cp-ival 1 --nofw --ma 12.0873719078613 --trim3 5 --score-min L,1.09241216250464,5.20806074640023 --mp 6.27920316333523,4.47329852554499 -r -p 4 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GT 671s GT 671s Processing line... 671s Processing line... 671s CTGGCGGGAAGACCGCGGCTCGGTCT 671s CTGGCGGGAAGACCGCGGCTCGGTCT 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GTGTTGAGAGGGTGACAGAGGCG 671s GTGTTGAGAGGGTGACAGAGGCG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s CCGC 671s CCGC 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s AGGCGGTCAGG 671s AGGCGGTCAGG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s TC 671s TC 671s Processing line... 671s Processing line... 671s ACC 671s ACC 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s CG 671s CG 671s Processing line... 671s Processing line... 671s Processing line... 671s --- Summary --- 671s Read 1 reference strings 671s Checked 11 alignments, 0 edits 671s --------------- 671s PASSED 671s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 671s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 671s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 671s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '4' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 671s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '9' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 671s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '20' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 671s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '22' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 671s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '23' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 671s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '24' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 671s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '26' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 671s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 671s Warning: skipping read '47' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 671s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '48' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 671s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '50' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 671s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '60' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 671s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 671s Warning: skipping read '65' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 671s 79 reads; of these: 671s 79 (100.00%) were unpaired; of these: 671s 68 (86.08%) aligned 0 times 671s 7 (8.86%) aligned exactly 1 time 671s 4 (5.06%) aligned >1 times 671s 13.92% overall alignment rate 671s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 671s Flattened IUPAC characters 671s Mutating sequence Sim.pm.2 671s Introducing 3 SNPs, 0/0 ref/read gaps, and 2 rearrangements 671s Finished SNPs 671s Finished ref gaps 671s Finished read gaps 671s Mutating sequence Sim.pm.1 671s Introducing 14 SNPs, 0/0 ref/read gaps, and 1 rearrangements 671s Finished SNPs 671s Finished ref gaps 671s Finished read gaps 671s Mutated reference genome to subject genome 671s SNPs introduced: 17 671s Reference gaps introduced: 0 671s Read gaps introduced: 0 671s Rearrangements introduced: 3 671s Created read sampler 671s Sampling 56 reads 671s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 671s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 671s parsing sequence Sim.pm.1... 671s *** Run 47 of 100 671s /usr/bin/bowtie2 --score-min L,3.53265063663726,3.23642827854324 -D 26 --mm --np 4 --cp-min 3 --mp 7.48301192235947,6.50408772744586 --rfg 46.6488167532484 --norc --trim5 4 --cp-ival 1 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq 671s parsing sequence Sim.pm.2... 671s Parsed 143 reference bases 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 671s 56 reads; of these: 671s 56 (100.00%) were unpaired; of these: 671s 47 (83.93%) aligned 0 times 671s 7 (12.50%) aligned exactly 1 time 671s 2 (3.57%) aligned >1 times 671s 16.07% overall alignment rate 671s Read 50 alignments... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s CCCAG 671s CCCAG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GTCTGCGCCCAGCTTAGGCGGTCAGG 671s GTCTGCGCCCAGCTTAGGCGGTCAGG 671s Processing line... 671s Processing line... 671s CCGGGTGGTGTTGAGAGGGT 671s CCGGGTGGTGTTGAGAGGGT 671s Processing line... 671s TGA 671s TGA 671s Processing line... 671s CGGCTCGGTCTGCGCCCA 671s CGGCTCGGTCTGCGCCCA 671s Processing line... 671s Processing line... 671s AGACC 671s AGACC 671s Processing line... 671s Processing line... 671s Processing line... 671s CGGTCAGGAGGGAG 671s CGGTCAGGAGGGAG 671s Processing line... 671s GTGGTGTTGAGAGGGTGACAG 671s GTGGTGTTGAGAGGGTGACAG 671s Processing line... 671s Processing line... 671s Processing line... 671s GGCGTGG 671s GGCGTGG 671s Processing line... 671s Processing line... 671s Processing line... 671s --- Summary --- 671s Read 1 reference strings 671s Checked 9 alignments, 0 edits 671s --------------- 671s PASSED 671s ALSO checking that bowtie2 and bowtie2-align match up 671s /usr/bin/bowtie2 --score-min L,3.53265063663726,3.23642827854324 -D 26 --mm --np 4 --cp-min 3 --mp 7.48301192235947,6.50408772744586 --rfg 46.6488167532484 --norc --trim5 4 --cp-ival 1 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 671s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 671s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 671s 56 reads; of these: 671s 56 (100.00%) were unpaired; of these: 671s 47 (83.93%) aligned 0 times 671s 7 (12.50%) aligned exactly 1 time 671s 2 (3.57%) aligned >1 times 671s 16.07% overall alignment rate 671s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 671s Flattened IUPAC characters 671s Mutating sequence Sim.pm.2 671s Introducing 12 SNPs, 0/2 ref/read gaps, and 0 rearrangements 671s Finished SNPs 671s Finished ref gaps 671s Finished read gaps 671s Mutating sequence Sim.pm.1 671s Introducing 11 SNPs, 0/2 ref/read gaps, and 0 rearrangements 671s Finished SNPs 671s Finished ref gaps 671s Finished read gaps 671s Mutated reference genome to subject genome 671s SNPs introduced: 23 671s Reference gaps introduced: 0 671s Read gaps introduced: 4 671s Rearrangements introduced: 0 671s Created read sampler 671s Sampling 156 reads 671s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 671s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 671s parsing sequence Sim.pm.1... 671s parsing sequence Sim.pm.2... 671s *** Run 48 of 100 671s /usr/bin/bowtie2 --cp-ival 1 -a --rfg 48.632629029813,17.4268593025781 --nofw --trim3 4 -N 0 -L29 --cp-min 2 --mm --ma 14.6662281549673 --score-min L,9.45662729712824,2.14223199760994 -R 3 --gbar 9 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 671s Parsed 143 reference bases 671s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 671s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #2 of read '2' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 671s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '3' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 671s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '6' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 671s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '13' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 671s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '14' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 671s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '15' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 671s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #2 of read '36' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 671s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '41' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 671s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '49' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 671s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '56' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 671s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '62' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 671s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '75' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 671s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '77' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 671s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '94' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 671s Read 50 alignments... 671s Read 100 alignments... 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 671s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '102' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 671s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '107' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 671s Warning: skipping mate #2 of read '116' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #2 of read '116' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 671s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '124' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 671s Warning: skipping mate #1 of read '125' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '125' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 671s Warning: skipping mate #1 of read '131' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '131' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 671s Warning: skipping mate #1 of read '133' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '133' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 671s Read 150 alignments... 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 671s Warning: skipping mate #1 of read '145' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '145' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 671s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '151' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 671s Read 200 alignments... 671s Read 250 alignments... 671s Read 300 alignments... 671s 156 reads; of these: 671s 143 (91.67%) were paired; of these: 671s 142 (99.30%) aligned concordantly 0 times 671s 0 (0.00%) aligned concordantly exactly 1 time 671s 1 (0.70%) aligned concordantly >1 times 671s ---- 671s 142 pairs aligned concordantly 0 times; of these: 671s 0 (0.00%) aligned discordantly 1 time 671s ---- 671s 142 pairs aligned 0 times concordantly or discordantly; of these: 671s 284 mates make up the pairs; of these: 671s 249 (87.68%) aligned 0 times 671s 21 (7.39%) aligned exactly 1 time 671s 14 (4.93%) aligned >1 times 671s 13 (8.33%) were unpaired; of these: 671s 10 (76.92%) aligned 0 times 671s 2 (15.38%) aligned exactly 1 time 671s 1 (7.69%) aligned >1 times 671s 13.38% overall alignment rate 671s Read 350 alignments... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s CCAGCT 671s CCAGCT 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GGGGGA 671s GGGGGA 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s CCGC 671s CCGC 671s Processing line... 671s Processing line... 671s CCCAGCTTAGGCGGTCA 671s CCCAGCTTAGGCGGTCA 671s Processing line... 671s Processing line... 671s Processing line... 671s TCC 671s TCC 671s Processing line... 671s TCC 671s TCC 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s GG 671s GG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s TGG 671s TGG 671s Processing line... 671s TGG 671s TGG 671s Processing line... 671s TGG 671s TGG 671s Processing line... 671s TGG 671s TGG 671s Processing line... 671s TGG 671s TGG 671s Processing line... 671s TGG 671s TGG 671s Processing line... 671s TGG 671s TGG 671s Processing line... 671s TGG 671s TGG 671s Processing line... 671s TGG 671s TGG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s TGAGAGGGTGA 671s TGAGAGGGTGA 671s Processing line... 671s Processing line... 671s CGGT 671s CGGT 671s Processing line... 671s CGGT 671s CGGT 671s Processing line... 671s Processing line... 671s Processing line... 671s GTGGTGTTGAGAGGGTGACAGAGGCGTGG 671s GTGGTGTTGAGAGGGTGACAGAGGCGTGG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GTTGAGAGGGTGACAGAGGCGTGG 671s GTTGAGAGGGTGACAGAGGCGTGG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s AGGGTGACAGAGGCGT 671s AGGGTGACAGAGGCGT 671s Processing line... 671s Processing line... 671s ACCG 671s ACCG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GTTGAGAGGG 671s GTTGAGAGGG 671s Processing line... 671s Processing line... 671s CCGGGTGGTGTTGAGAGGGTGACAGAGGCGTGG 671s CCGGGTGGTGTTGAGAGGGTGACAGAGGCGTGG 671s Processing line... 671s Processing line... 671s CCGGGTGGTGTT 671s CCGGGTGGTGTT 671s Processing line... 671s CCGGGTGGTGTT 671s CCGGGTGGTGTT 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s TGC 671s TGC 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s CCG 671s CCG 671s Processing line... 671s CCG 671s CCG 671s Processing line... 671s CCG 671s CCG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s CCGGGTGGT 671s CCGGGTGGT 671s Processing line... 671s CCGGGTGGT 671s CCGGGTGGT 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s CGGGTGGTGTTGAGAGGGTGACAGA 671s CGGGTGGTGTTGAGAGGGTGACAGA 671s Processing line... 671s Processing line... 671s CC 671s CC 671s Processing line... 671s CC 671s CC 671s Processing line... 671s CC 671s CC 671s Processing line... 671s CC 671s CC 671s Processing line... 671s CC 671s CC 671s Processing line... 671s CCC 671s CCC 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s CGGGTG 671s CGGGTG 671s Processing line... 671s CGGGTG 671s CGGGTG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GGG 671s GGG 671s Processing line... 671s GGG 671s GGG 671s Processing line... 671s GGG 671s GGG 671s Processing line... 671s GGG 671s GGG 671s Processing line... 671s GGG 671s GGG 671s Processing line... 671s GGG 671s GGG 671s Processing line... 671s GGG 671s GGG 671s Processing line... 671s GGG 671s GGG 671s Processing line... 671s GGG 671s GGG 671s Processing line... 671s GGG 671s GGG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GGGGGGGACTGGCGGGAAGACCGCGGCT 671s GGGGGGGACTGGCGGGAAGACCGCGGCT 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GTGGT 671s GTGGT 671s Processing line... 671s GTGGT 671s GTGGT 671s Processing line... 671s GTGGT 671s GTGGT 671s Processing line... 671s GTGGT 671s GTGGT 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GGGTGAC 671s GGGTGAC 671s Processing line... 671s Processing line... 671s GGGTGGTGTTGAGAGGGTGACAGAGG 671s GGGTGGTGTTGAGAGGGTGACAGAGG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s AAGACCGCG 671s AAGACCGCG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GGTGGTGTTGAGAGG 671s GGTGGTGTTGAGAGG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s AC 671s AC 671s Processing line... 671s AC 671s AC 671s Processing line... 671s AC 671s AC 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GTGTTGAGAGG 671s GTGTTGAGAGG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s TGGTG 671s TGGTG 671s Processing line... 671s TGGTG 671s TGGTG 671s Processing line... 671s TGGTG 671s TGGTG 671s Processing line... 671s TGGTG 671s TGGTG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GACTGGCG 671s GACTGGCG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s AGAGGGTG 671s AGAGGGTG 671s Processing line... 671s Processing line... 671s Processing line... 671s GGGTGGTGTTGAGAGGG 671s GGGTGGTGTTGAGAGGG 671s Processing line... 671s Processing line... 671s Processing line... 671s GTGACAGAGGCGTGG 671s GTGACAGAGGCGTGG 671s Processing line... 671s TC 671s TC 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s CG 671s CG 671s Processing line... 671s CG 671s CG 671s Processing line... 671s CG 671s CG 671s Processing line... 671s CG 671s CG 671s Processing line... 671s CG 671s CG 671s Processing line... 671s CG 671s CG 671s Processing line... 671s CG 671s CG 671s Processing line... 671s CG 671s CG 671s Processing line... 671s CG 671s CG 671s Processing line... 671s CG 671s CG 671s Processing line... 671s Processing line... 671s Processing line... 671s Processing line... 671s GGTG 671s GGTG 671s Processing line... 671s GGTG 671s GGTG 671s Processing line... 671s GGTG 671s GGTG 671s Processing line... 671s GGTG 671s GGTG 671s Processing line... 671s GGTG 671s GGTG 671s Processing line... 671s GGTG 671s GGTG 671s Processing line... 671s GGTG 671s GGTG 671s Processing line... 671s --- Summary --- 671s Read 1 reference strings 671s Checked 122 alignments, 0 edits 671s --------------- 671s PASSED 671s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 671s /usr/bin/bowtie2 --cp-ival 1 -a --rfg 48.632629029813,17.4268593025781 --nofw --trim3 4 -N 0 -L29 --cp-min 2 --mm --ma 14.6662281549673 --score-min L,9.45662729712824,2.14223199760994 -R 3 --gbar 9 -q -p 2 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 671s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 671s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #2 of read '2' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 671s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '3' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 671s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '6' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 671s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '13' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 671s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '14' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 671s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '15' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 671s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #2 of read '36' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 671s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '41' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 671s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '49' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 671s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '56' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 671s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '62' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 671s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '75' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 671s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '77' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 671s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '102' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 671s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '94' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 671s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '107' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 671s Warning: skipping mate #2 of read '116' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #2 of read '116' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 671s Warning: skipping mate #1 of read '131' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '131' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 671s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '124' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 671s Warning: skipping mate #1 of read '133' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '133' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 671s Warning: skipping mate #1 of read '125' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '125' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 671s Warning: skipping mate #1 of read '145' because length (1) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '145' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 671s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 671s Warning: skipping mate #1 of read '151' because it was < 2 characters long 671s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 671s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 671s 156 reads; of these: 671s 143 (91.67%) were paired; of these: 671s 142 (99.30%diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 671s ) aligned concordantly 0 times 671s 0 (0.00%) aligned concordantly exactly 1 time 671s 1 (0.70%) aligned concordantly >1 times 671s ---- 671s 142 pairs aligned concordantly 0 times; of these: 671s 0 (0.00%) aligned discordantly 1 time 671s ---- 671s 142 pairs aligned 0 times concordantly or discordantly; of these: 671s 284 mates make up the pairs; of these: 671s 249 (87.68%) aligned 0 times 671s 21 (7.39%) aligned exactly 1 time 671s 14 (4.93%) aligned >1 times 671s 13 (8.33%) were unpaired; of these: 671s 10 (76.92%) aligned 0 times 671s 2 (15.38%) aligned exactly 1 time 671s 1 (7.69%) aligned >1 times 671s 13.38% overall alignment rate 671s *** Run 49 of 100 671s /usr/bin/bowtie2 --score-min L,2.64406630012469,7.40899729205518 -k 13 --mp 8.14744191781272,5.26271835962826 --cp-min 3 --norc --trim5 2 --local --cp-ival 1 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 671s Flattened IUPAC characters 671s Mutating sequence Sim.pm.2 671s Introducing 9 SNPs, 0/0 ref/read gaps, and 1 rearrangements 671s Finished SNPs 671s Finished ref gaps 671s Finished read gaps 671s Mutating sequence Sim.pm.1 671s Introducing 6 SNPs, 3/0 ref/read gaps, and 1 rearrangements 671s Finished SNPs 671s Finished ref gaps 671s Finished read gaps 671s Mutated reference genome to subject genome 671s SNPs introduced: 15 671s Reference gaps introduced: 3 671s Read gaps introduced: 0 671s Rearrangements introduced: 2 671s Created read sampler 671s Sampling 78 reads 671s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 671s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 671s parsing sequence Sim.pm.1... 671s parsing sequence Sim.pm.2... 671s Parsed 143 reference bases 672s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 672s Warning: skipping mate #1 of read '1' because it was < 2 characters long 672s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 672s Warning: skipping mate #1 of read '6' because it was < 2 characters long 672s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 672s Warning: skipping mate #1 of read '30' because it was < 2 characters long 672s Warning: skipping mate #1 of read '40' because length (1) <= # seed mismatches (0) 672s Warning: skipping mate #1 of read '40' because it was < 2 characters long 672s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 672s Warning: skipping mate #2 of read '52' because it was < 2 characters long 672s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 672s Warning: skipping mate #1 of read '54' because it was < 2 characters long 672s Read 50 alignments... 672s Read 100 alignments... 672s 78 reads; of these: 672s 73 (93.59%) were paired; of these: 672s 73 (100.00%) aligned concordantly 0 times 672s 0 (0.00%) aligned concordantly exactly 1 time 672s 0 (0.00%) aligned concordantly >1 times 672s ---- 672s 73 pairs aligned concordantly 0 times; of these: 672s 0 (0.00%) aligned discordantly 1 time 672s ---- 672s 73 pairs aligned 0 times concordantly or discordantly; of these: 672s 146 mates make up the pairs; of these: 672s 146 (100.00%) aligned 0 times 672s 0 (0.00%) aligned exactly 1 time 672s 0 (0.00%) aligned >1 times 672s 5 (6.41%) were unpaired; of these: 672s 5 (100.00%) aligned 0 times 672s 0 (0.00%) aligned exactly 1 time 672s 0 (0.00%) aligned >1 times 672s 0.00% overall alignment rate 672s Read 150 alignments... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s /usr/bin/bowtie2 --score-min L,2.64406630012469,7.40899729205518 -k 13 --mp 8.14744191781272,5.26271835962826 --cp-min 3 --norc --trim5 2 --local --cp-ival 1 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s --- Summary --- 672s Read 1 reference strings 672s Checked 0 alignments, 0 edits 672s --------------- 672s PASSED 672s ALSO checking that bowtie2 and bowtie2-align match up 672s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 672s Warning: skipping mate #1 of read '1' because it was < 2 characters long 672s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 672s Warning: skipping mate #1 of read '6' because it was < 2 characters long 672s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 672s Warning: skipping mate #1 of read '30' because it was < 2 characters long 672s Warning: skipping mate #1 of read '40' because length (1) <= # seed mismatches (0) 672s Warning: skipping mate #1 of read '40' because it was < 2 characters long 672s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 672s Warning: skipping mate #2 of read '52' because it was < 2 characters long 672s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 672s Warning: skipping mate #1 of read '54' because it was < 2 characters long 672s 78 reads; of these: 672s 73 (93.59%) were paired; of these: 672s 73 (100.00%) aligned concordantly 0 times 672s 0 (0.00%) aligned concordantly exactly 1 time 672s 0 (0.00%) aligned concordantly >1 times 672s ---- 672s 73 pairs aligned concordantly 0 times; of these: 672s 0 (0.00%) aligned discordantly 1 time 672s ---- 672s 73 pairs aligned 0 times concordantly or discordantly; of these: 672s 146 mates make up the pairs; of these: 672s 146 (100.00%) aligned 0 times 672s 0 (0.00%) aligned exactly 1 time 672s 0 (0.00%) aligned >1 times 672s 5 (6.41%) were unpaired; of these: 672s 5 (100.00%) aligned 0 times 672s 0 (0.00%) aligned exactly 1 time 672s 0 (0.00%) aligned >1 times 672s 0.00% overall alignment rate 672s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 672s Flattened IUPAC characters 672s Mutating sequence Sim.pm.1 672s Introducing 7 SNPs, 0/1 ref/read gaps, and 1 rearrangements 672s Finished SNPs 672s Finished ref gaps 672s Finished read gaps 672s Mutating sequence Sim.pm.2 672s Introducing 7 SNPs, 0/1 ref/read gaps, and 1 rearrangements 672s Finished SNPs 672s Finished ref gaps 672s Finished read gaps 672s Mutated reference genome to subject genome 672s SNPs introduced: 14 672s Reference gaps introduced: 0 672s Read gaps introduced: 2 672s Rearrangements introduced: 2 672s Created read sampler 672s Sampling 78 reads 672s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 672s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 672s *** Run 50 of 100 672s /usr/bin/bowtie2 -D 21 --score-min L,7.19659208725688,9.24547002365112 --mm --rdg 11.5184692917717,1.75284527940296 --np 2 --cp-min 3 --mp 4.33858968959196,1.02036705321223 --rfg 45.6116651175504 --trim5 5 --norc -M 2 --cp-ival 2 --local -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw 672s parsing sequence Sim.pm.1... 672s parsing sequence Sim.pm.2... 672s Parsed 143 reference bases 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '5' because it was < 2 characters long 672s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '20' because it was < 2 characters long 672s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '22' because it was < 2 characters long 672s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '23' because it was < 2 characters long 672s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '24' because it was < 2 characters long 672s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 672s Warning: skipping read '29' because it was < 2 characters long 672s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '32' because it was < 2 characters long 672s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '39' because it was < 2 characters long 672s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 672s Warning: skipping read '42' because it was < 2 characters long 672s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '44' because it was < 2 characters long 672s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '45' because it was < 2 characters long 672s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '51' because it was < 2 characters long 672s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '55' because it was < 2 characters long 672s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '64' because it was < 2 characters long 672s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '65' because it was < 2 characters long 672s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '67' because it was < 2 characters long 672s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '74' because it was < 2 characters long 672s 78 reads; of these: 672s 78 (100.00%) were unpaired; of these: 672s 78 (100.00%) aligned 0 times 672s 0 (0.00%) aligned exactly 1 time 672s 0 (0.00%) aligned >1 times 672s 0.00% overall alignment rate 672s Read 50 alignments... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s --- Summary --- 672s Read 1 reference strings 672s /usr/bin/bowtie2 -D 21 --score-min L,7.19659208725688,9.24547002365112 --mm --rdg 11.5184692917717,1.75284527940296 --np 2 --cp-min 3 --mp 4.33858968959196,1.02036705321223 --rfg 45.6116651175504 --trim5 5 --norc -M 2 --cp-ival 2 --local -r -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 672s Checked 0 alignments, 0 edits 672s --------------- 672s PASSED 672s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '5' because it was < 2 characters long 672s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '20' because it was < 2 characters long 672s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '22' because it was < 2 characters long 672s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '23' because it was < 2 characters long 672s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '24' because it was < 2 characters long 672s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 672s Warning: skipping read '29' because it was < 2 characters long 672s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '32' because it was < 2 characters long 672s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '39' because it was < 2 characters long 672s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 672s Warning: skipping read '42' because it was < 2 characters long 672s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '44' because it was < 2 characters long 672s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '45' because it was < 2 characters long 672s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '51' because it was < 2 characters long 672s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '55' because it was < 2 characters long 672s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '64' because it was < 2 characters long 672s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '65' because it was < 2 characters long 672s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '67' because it was < 2 characters long 672s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '74' because it was < 2 characters long 672s 78 reads; of these: 672s 78 (100.00%) were unpaired; of these: 672s 78 (100.00%) aligned 0 times 672s 0 (0.00%) aligned exactly 1 time 672s 0 (0.00%) aligned >1 times 672s 0.00% overall alignment rate 672s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 672s Flattened IUPAC characters 672s Mutating sequence Sim.pm.1 672s Introducing 9 SNPs, 1/1 ref/read gaps, and 2 rearrangements 672s Finished SNPs 672s Finished ref gaps 672s Finished read gaps 672s Mutating sequence Sim.pm.2 672s Introducing 6 SNPs, 0/2 ref/read gaps, and 1 rearrangements 672s Finished SNPs 672s Finished ref gaps 672s Finished read gaps 672s Mutated reference genome to subject genome 672s SNPs introduced: 15 672s Reference gaps introduced: 1 672s Read gaps introduced: 3 672s Rearrangements introduced: 3 672s Created read sampler 672s Sampling 27 reads 672s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 672s *** Run 51 of 100 672s /usr/bin/bowtie2 --mm -k 7 --score-min L,7.33802714512325,3.61599060816653 --ma 10.6638170994932 --np 2 --cp-min 10 --rfg 6.07915602006403,2.54441886268351 --mp 9.72496423154229,9.11456003400386 -N 1 -L16 --trim3 9 --nofw --cp-ival 1 --trim5 2 -q -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq 672s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 672s parsing sequence Sim.pm.1... 672s parsing sequence Sim.pm.2... 672s Parsed 143 reference bases 672s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 672s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 672s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '11' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 672s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '12' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 672s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '15' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 672s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '17' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 672s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '19' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 672s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '20' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 672s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '22' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 672s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '24' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 672s Warning: skipping read '25' because length (1) <= # seed mismatches (1) 672s Warning: skipping read '25' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 672s /usr/bin/bowtie2 --mm -k 7 --score-min L,7.33802714512325,3.61599060816653 --ma 10.6638170994932 --np 2 --cp-min 10 --rfg 6.07915602006403,2.54441886268351 --mp 9.72496423154229,9.11456003400386 -N 1 -L16 --trim3 9 --nofw --cp-ival 1 --trim5 2 -q -p 2 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 672s 27 reads; of these: 672s 27 (100.00%) were unpaired; of these: 672s 23 (85.19%) aligned 0 times 672s 2 (7.41%) aligned exactly 1 time 672s 2 (7.41%) aligned >1 times 672s 14.81% overall alignment rate 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s GACAGAGG 672s GACAGAGG 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s GGT 672s GGT 672s Processing line... 672s GGT 672s GGT 672s Processing line... 672s GGT 672s GGT 672s Processing line... 672s GGT 672s GGT 672s Processing line... 672s GGT 672s GGT 672s Processing line... 672s GGT 672s GGT 672s Processing line... 672s GGT 672s GGT 672s Processing line... 672s Processing line... 672s Processing line... 672s GAGAGGGT 672s GAGAGGGT 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s TGGTGG 672s TGGTGG 672s Processing line... 672s TGGTGG 672s TGGTGG 672s --- Summary --- 672s Read 1 reference strings 672s Checked 11 alignments, 0 edits 672s --------------- 672s PASSED 672s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 672s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 672s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 672s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '11' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 672s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '12' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 672s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '15' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 672s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '17' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 672s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '19' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 672s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '20' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 672s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '22' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 672s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 672s Warning: skipping read '24' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 672s Warning: skipping read '25' because length (1) <= # seed mismatches (1) 672s Warning: skipping read '25' because it was < 2 characters long 672s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 672s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 672s 27 reads; of these: 672s 27 (100.00%) were unpaired; of these: 672s 23 (85.19%) aligned 0 times 672s 2 (7.41%) aligned exactly 1 time 672s 2 (7.41%) aligned >1 times 672s 14.81% overall alignment rate 672s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 672s Flattened IUPAC characters 672s Mutating sequence Sim.pm.2 672s Introducing 20 SNPs, 4/1 ref/read gaps, and 2 rearrangements 672s Finished SNPs 672s Finished ref gaps 672s Finished read gaps 672s Mutating sequence Sim.pm.1 672s Introducing 12 SNPs, 1/2 ref/read gaps, and 1 rearrangements 672s Finished SNPs 672s Finished ref gaps 672s Finished read gaps 672s Mutated reference genome to subject genome 672s SNPs introduced: 32 672s Reference gaps introduced: 5 672s Read gaps introduced: 3 672s Rearrangements introduced: 3 672s Created read sampler 672s Sampling 65 reads 672s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 672s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 672s parsing sequence Sim.pm.1... 672s parsing sequence Sim.pm.2... 672s Parsed 143 reference bases 672s *** Run 52 of 100 672s /usr/bin/bowtie2 --mm --rfg 32.3814797035539 -R 1 --score-min L,2.14689944381195,7.10851595887163 --trim3 9 --cp-ival 1 --local --trim5 2 -a --cp-min 2 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 672s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '5' because it was < 2 characters long 672s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '15' because it was < 2 characters long 672s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '16' because it was < 2 characters long 672s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '19' because it was < 2 characters long 672s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '25' because it was < 2 characters long 672s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '32' because it was < 2 characters long 672s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 672s Warning: skipping read '38' because it was < 2 characters long 672s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '39' because it was < 2 characters long 672s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '43' because it was < 2 characters long 672s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '44' because it was < 2 characters long 672s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '47' because it was < 2 characters long 672s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '52' because it was < 2 characters long 672s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '54' because it was < 2 characters long 672s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 672s Warning: skipping read '58' because it was < 2 characters long 672s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '60' because it was < 2 characters long 672s 65 reads; of these: 672s 65 (100.00%) were unpaired; of these: 672s 65 (100.00%) aligned 0 times 672s 0 (0.00%) aligned exactly 1 time 672s 0 (0.00%) aligned >1 times 672s 0.00% overall alignment rate 672s Read 50 alignments... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s /usr/bin/bowtie2 --mm --rfg 32.3814797035539 -R 1 --score-min L,2.14689944381195,7.10851595887163 --trim3 9 --cp-ival 1 --local --trim5 2 -a --cp-min 2 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s Processing line... 672s --- Summary --- 672s Read 1 reference strings 672s Checked 0 alignments, 0 edits 672s --------------- 672s PASSED 672s ALSO checking that bowtie2 and bowtie2-align match up 672s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '5' because it was < 2 characters long 672s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '15' because it was < 2 characters long 672s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '16' because it was < 2 characters long 672s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '19' because it was < 2 characters long 672s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '25' because it was < 2 characters long 672s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '32' because it was < 2 characters long 672s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 672s Warning: skipping read '38' because it was < 2 characters long 672s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '39' because it was < 2 characters long 672s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '43' because it was < 2 characters long 672s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '44' because it was < 2 characters long 672s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '47' because it was < 2 characters long 672s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '52' because it was < 2 characters long 672s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '54' because it was < 2 characters long 672s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 672s Warning: skipping read '58' because it was < 2 characters long 672s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 672s Warning: skipping read '60' because it was < 2 characters long 672s 65 reads; of these: 672s 65 (100.00%) were unpaired; of these: 672s 65 (100.00%) aligned 0 times 672s 0 (0.00%) aligned exactly 1 time 672s 0 (0.00%) aligned >1 times 672s 0.00% overall alignment rate 672s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 672s Flattened IUPAC characters 672s Mutating sequence Sim.pm.1 672s Introducing 3 SNPs, 0/4 ref/read gaps, and 1 rearrangements 672s Finished SNPs 672s Finished ref gaps 672s Finished read gaps 672s Mutating sequence Sim.pm.2 672s Introducing 12 SNPs, 1/1 ref/read gaps, and 1 rearrangements 672s Finished SNPs 672s Finished ref gaps 672s Finished read gaps 672s Mutated reference genome to subject genome 672s SNPs introduced: 15 672s Reference gaps introduced: 1 672s Read gaps introduced: 5 672s Rearrangements introduced: 2 672s Created read sampler 672s Sampling 26 reads 672s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 672s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 672s parsing sequence Sim.pm.1... 672s parsing sequence Sim.pm.2... 672s Parsed 143 reference bases 672s *** Run 53 of 100 672s /usr/bin/bowtie2 --cp-min 3 --np 3 --mm --gbar 2 -R 3 --score-min L,7.32941499492166,8.35899459082379 --cp-ival 2 --trim5 0 -a --rfg 28.9797188515198 -N 0 --mp 4.80637391728432,4.42920704348134 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 673s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 673s 26 reads; of these: 673s 26 (100.00%) were unpaired; of these: 673s 21 (80.77%) aligned 0 times 673s 2 (7.69%) aligned exactly 1 time 673s 3 (11.54%) aligned >1 times 673s 19.23% overall alignment rate 673s Read 50 alignments... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s CC 673s CC 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s CC 673s CC 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s /usr/bin/bowtie2 --cp-min 3 --np 3 --mm --gbar 2 -R 3 --score-min L,7.32941499492166,8.35899459082379 --cp-ival 2 --trim5 0 -a --rfg 28.9797188515198 -N 0 --mp 4.80637391728432,4.42920704348134 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 673s Processing line... 673s GG 673s GG 673s Processing line... 673s CC 673s CC 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s CC 673s CC 673s Processing line... 673s GG 673s GG 673s Processing line... 673s CC 673s CC 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GG 673s GG 673s Processing line... 673s GGC 673s GGC 673s Processing line... 673s GCC 673s GCC 673s Processing line... 673s GGC 673s GGC 673s Processing line... 673s GGC 673s GGC 673s Processing line... 673s GGC 673s GGC 673s Processing line... 673s GGC 673s GGC 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GAGGCGTGG 673s GAGGCGTGG 673s Processing line... 673s GAGGCGTGG 673s GAGGCGTGG 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GCTCGGT 673s GCTCGGT 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s TCGG 673s TCGG 673s Processing line... 673s --- Summary --- 673s Read 1 reference strings 673s Checked 47 alignments, 0 edits 673s --------------- 673s PASSED 673s ALSO checking that bowtie2 and bowtie2-align match up 673s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 673s 26 reads; of these: 673s 26 (100.00%) were unpaired; of these: 673s 21 (80.77%) aligned 0 times 673s 2 (7.69%) aligned exactly 1 time 673s 3 (11.54%) aligned >1 times 673s 19.23% overall alignment rate 673s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 673s /usr/bin/bowtie2 --cp-min 3 --np 3 --mm --gbar 2 -R 3 --score-min L,7.32941499492166,8.35899459082379 --cp-ival 2 --trim5 0 -a --rfg 28.9797188515198 -N 0 --mp 4.80637391728432,4.42920704348134 -f -p 2 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 673s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 673s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 673s 26 reads; of these: 673s 26 (100.00%) were unpaired; of these: 673s 21 (80.77%) aligned 0 times 673s 2 (7.69%) aligned exactly 1 time 673s 3 (11.54%) aligned >1 times 673s 19.23% overall alignment rate 673s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 673s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 673s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 673s *** Run 54 of 100 673s /usr/bin/bowtie2 --mm --score-min L,6.47310175803194,5.18173281869259 --ma 17.1226453121867 -D 34 -k 9 -R 4 --cp-min 3 --nofw --trim3 8 --mp 4.84485625886022,3.8285828216139 --cp-ival 3 --n-ceil 0.893737560123062,0.746549135752338 --norc -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta 673s Flattened IUPAC characters 673s Mutating sequence Sim.pm.2 673s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 673s Finished SNPs 673s Finished ref gaps 673s Finished read gaps 673s Mutating sequence Sim.pm.1 673s Introducing 5 SNPs, 3/1 ref/read gaps, and 1 rearrangements 673s Finished SNPs 673s Finished ref gaps 673s Finished read gaps 673s Mutated reference genome to subject genome 673s SNPs introduced: 13 673s Reference gaps introduced: 3 673s Read gaps introduced: 1 673s Rearrangements introduced: 1 673s Created read sampler 673s Sampling 140 reads 673s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 673s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 673s parsing sequence Sim.pm.1... 673s parsing sequence Sim.pm.2... 673s Parsed 143 reference bases 673s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 673s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '7' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 673s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '10' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 673s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '21' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 673s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '22' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 673s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '23' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 673s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '25' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 673s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 673s Warning: skipping mate #2 of read '27' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 673s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '30' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 673s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '32' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 673s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '41' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 673s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '44' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 673s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '48' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 673s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '52' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 673s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '57' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 673s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '66' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 673s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '71' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 673s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '77' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 673s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '80' because it was < 2 characters long 673s Read 50 alignments... 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 673s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '82' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 673s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '85' because it was < 2 characters long 673s Warning: skipping mate #2 of read '85' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 673s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '92' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 673s Warning: skipping mate #2 of read '100' because length (1) <= # seed mismatches (0) 673s Warning: skipping mate #2 of read '100' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 673s Warning: skipping mate #1 of read '106' because length (1) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '106' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 673s Warning: skipping mate #2 of read '109' because length (1) <= # seed mismatches (0) 673s Warning: skipping mate #2 of read '109' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 673s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '112' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 673s Warning: skipping read '119' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '119' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 673s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '120' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 673s Warning: skipping mate #1 of read '121' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '121' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 673s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '122' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 673s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '123' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 673s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '126' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 673s Warning: skipping mate #2 of read '132' because length (1) <= # seed mismatches (0) 673s Warning: skipping mate #2 of read '132' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 673s Warning: skipping mate #1 of read '136' because length (1) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '136' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 673s Warning: skipping mate #1 of read '139' because length (0) <= # seed mismatches (0) 673s Warning: skipping mate #1 of read '139' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 673s Read 100 alignments... 673s *** Run 55 of 100 673s /usr/bin/bowtie2 --cp-ival 2 -a --cp-min 4 --np 24 --norc --mm --score-min L,9.93877042121975,7.8280926180947 --trim3 7 --ma 1.04752404756823 -D 45 -N 0 -L17 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 673s 140 reads; of these: 673s 119 (85.00%) were paired; of these: 673s 119 (100.00%) aligned concordantly 0 times 673s 0 (0.00%) aligned concordantly exactly 1 time 673s 0 (0.00%) aligned concordantly >1 times 673s ---- 673s 119 pairs aligned concordantly 0 times; of these: 673s 0 (0.00%) aligned discordantly 1 time 673s ---- 673s 119 pairs aligned 0 times concordantly or discordantly; of these: 673s 238 mates make up the pairs; of these: 673s 238 (100.00%) aligned 0 times 673s 0 (0.00%) aligned exactly 1 time 673s 0 (0.00%) aligned >1 times 673s 21 (15.00%) were unpaired; of these: 673s 21 (100.00%) aligned 0 times 673s 0 (0.00%) aligned exactly 1 time 673s 0 (0.00%) aligned >1 times 673s 0.00% overall alignment rate 673s Read 150 alignments... 673s Read 200 alignments... 673s Read 250 alignments... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing 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line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s --- Summary --- 673s Read 1 reference strings 673s Checked 0 alignments, 0 edits 673s --------------- 673s PASSED 673s Flattened IUPAC characters 673s Mutating sequence Sim.pm.1 673s Introducing 21 SNPs, 3/1 ref/read gaps, and 1 rearrangements 673s Finished SNPs 673s Finished ref gaps 673s Finished read gaps 673s Mutating sequence Sim.pm.2 673s Introducing 13 SNPs, 0/0 ref/read gaps, and 0 rearrangements 673s Finished SNPs 673s Finished ref gaps 673s Finished read gaps 673s Mutated reference genome to subject genome 673s SNPs introduced: 34 673s Reference gaps introduced: 3 673s Read gaps introduced: 1 673s Rearrangements introduced: 1 673s Created read sampler 673s Sampling 196 reads 673s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 673s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 673s parsing sequence Sim.pm.1... 673s parsing sequence Sim.pm.2... 673s Parsed 143 reference bases 673s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 673s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 673s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '7' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 673s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '8' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 673s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '13' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 673s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '14' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 673s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '18' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 673s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '21' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 673s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '24' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 673s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '29' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 673s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '31' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 673s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '35' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 673s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '43' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 673s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '48' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 673s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '64' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 673s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '67' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 673s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '73' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 673s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '79' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 673s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '87' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 673s Warning: skipping read '90' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '90' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 673s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '93' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 673s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '94' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 673s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '95' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 673s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '98' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 673s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '99' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 673s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '100' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 673s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '103' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 673s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '107' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 673s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '108' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 673s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '110' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 673s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '113' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 673s Warning: skipping read '119' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '119' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 673s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '122' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 673s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '127' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 673s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '132' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 673s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '146' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 673s Warning: skipping read '147' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '147' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 673s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '152' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 673s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '154' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 673s Read 50 alignments... 673s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 673s Warning: skipping read '163' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '163' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 673s Warning: skipping read '164' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '164' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 673s Warning: skipping read '166' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '166' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 673s Warning: skipping read '177' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '177' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '178; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '179; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 673s Warning: skipping read '180' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '180' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '181; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '182; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '183; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '184; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '185; setting to 0 instead 673s Warning: skipping read '185' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '185' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '189; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '190; setting to 0 instead 673s Warning: skipping read '190' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '190' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '191; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '192; setting to 0 instead 673s Warning: skipping read '192' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '192' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '193; setting to 0 instead 673s Warning: skipping read '193' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '193' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '194; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '195; setting to 0 instead 673s Warning: skipping read '195' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '195' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '196; setting to 0 instead 673s Read 100 alignments... 673s Read 150 alignments... 673s 196 reads; of these: 673s 196 (100.00%) were unpaired; of these: 673s 180 (91.84%) aligned 0 times 673s 10 (5.10%) aligned exactly 1 time 673s 6 (3.06%) aligned >1 times 673s 8.16% overall alignment rate 673s Read 200 alignments... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s /usr/bin/bowtie2 --cp-ival 2 -a --cp-min 4 --np 24 --norc --mm --score-min L,9.93877042121975,7.8280926180947 --trim3 7 --ma 1.04752404756823 -D 45 -N 0 -L17 -f -p 3 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 673s Processing line... 673s TGAGA 673s TGAGA 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s TCG 673s TCG 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s CGCCCAGCTTA 673s CGCCCAGCTTA 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GTGTTGAGA 673s GTGTTGAGA 673s Processing line... 673s TGA 673s TGA 673s Processing line... 673s TGA 673s TGA 673s Processing line... 673s TGA 673s TGA 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GTGG 673s GTGG 673s Processing line... 673s GTGG 673s GTGG 673s Processing line... 673s GTGG 673s GTGG 673s Processing line... 673s GTGG 673s GTGG 673s Processing line... 673s GTGG 673s GTGG 673s Processing line... 673s GTGG 673s GTGG 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s CC 673s CC 673s Processing line... 673s CC 673s CC 673s Processing line... 673s CC 673s CC 673s Processing line... 673s CC 673s CC 673s Processing line... 673s CC 673s CC 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s TT 673s TT 673s Processing line... 673s TT 673s TT 673s Processing line... 673s TT 673s TT 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s AGAGGGTGAC 673s AGAGGGTGAC 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GGCT 673s GGCT 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s TCGGTCTGCGCCCAGCTTAGGCGGTCA 673s TCGGTCTGCGCCCAGCTTAGGCGGTCA 673s Processing line... 673s Processing line... 673s Processing line... 673s TGAGAGGGT 673s TGAGAGGGT 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s CGC 673s CGC 673s Processing line... 673s CGC 673s CGC 673s Processing line... 673s Processing line... 673s Processing line... 673s CCC 673s CCC 673s Processing line... 673s Processing line... 673s Processing line... 673s TCCGGGTGGTGTTGAGAG 673s TCCGGGTGGTGTTGAGAG 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s CG 673s CG 673s Processing line... 673s CG 673s CG 673s Processing line... 673s CG 673s CG 673s Processing line... 673s CG 673s CG 673s Processing line... 673s CG 673s CG 673s Processing line... 673s CG 673s CG 673s Processing line... 673s CG 673s CG 673s Processing line... 673s CG 673s CG 673s Processing line... 673s CG 673s CG 673s Processing line... 673s CG 673s CG 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s --- Summary --- 673s Read 1 reference strings 673s Checked 39 alignments, 0 edits 673s --------------- 673s PASSED 673s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 673s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 673s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 673s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '7' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 673s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '8' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 673s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '13' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 673s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '14' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 673s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '18' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 673s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '21' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 673s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '24' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 673s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '29' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 673s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '31' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 673s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '35' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 673s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '43' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 673s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '48' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 673s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '64' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 673s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '67' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 673s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '73' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 673s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '79' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 673s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '87' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 673s Warning: skipping read '90' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '90' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 673s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '93' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 673s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '94' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 673s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '95' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 673s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '98' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 673s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '99' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 673s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '100' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 673s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '103' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 673s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '107' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 673s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '108' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 673s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '110' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 673s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '113' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 673s Warning: skipping read '119' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '119' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 673s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '122' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 673s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '127' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 673s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '132' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 673s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '146' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 673s Warning: skipping read '147' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '147' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 673s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '152' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 673s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '154' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 673s Warning: skipping read '163' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '163' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 673s Warning: skipping read '164' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '164' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 673s Warning: skipping read '166' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '166' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 673s Warning: skipping read '177' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '177' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '178; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '179; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 673s Warning: skipping read '180' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '180' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '181; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '182; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '183; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '184; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '185; setting to 0 instead 673s Warning: skipping read '185' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '185' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '189; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '190; setting to 0 instead 673s Warning: skipping read '190' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '190' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '191; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '192; setting to 0 instead 673s Warning: skipping read '192' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '192' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '193; setting to 0 instead 673s Warning: skipping read '193' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '193' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '194; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '195; setting to 0 instead 673s Warning: skipping read '195' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '195' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '196; setting to 0 instead 673s 196 reads; of these: 673s 196 (100.00%) were unpaired; of these: 673s 180 (91.84%) aligned 0 times 673s 10 (5.10%) aligned exactly 1 time 673s 6 (3.06%) aligned >1 times 673s 8.16% overall alignment rate 673s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 673s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 673s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 673s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 673s /usr/bin/bowtie2 --cp-ival 2 -a --cp-min 4 --np 24 --norc --mm --score-min L,9.93877042121975,7.8280926180947 --trim3 7 --ma 1.04752404756823 -D 45 -N 0 -L17 -f -p 2 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 673s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 673s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 673s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '7' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 673s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '8' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 673s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '13' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 673s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '14' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 673s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '18' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 673s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '21' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 673s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '24' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 673s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '29' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 673s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '31' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 673s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '35' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 673s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '43' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 673s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '48' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 673s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '64' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 673s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '67' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 673s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '73' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 673s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '79' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 673s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '87' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 673s Warning: skipping read '90' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '90' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 673s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '93' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 673s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '94' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 673s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '95' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 673s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '98' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 673s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '99' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 673s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '100' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 673s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '103' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 673s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '107' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 673s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '108' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 673s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '110' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 673s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '113' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 673s Warning: skipping read '119' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '119' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 673s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '122' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 673s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '127' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 673s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '132' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 673s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '146' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 673s Warning: skipping read '147' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '147' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 673s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '152' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 673s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '154' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 673s Warning: skipping read '163' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '163' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 673s Warning: skipping read '164' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '164' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 673s Warning: skipping read '166' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '166' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 673s Warning: skipping read '177' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '177' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '178; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '179; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 673s Warning: skipping read '180' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '180' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '181; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '182; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '183; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '184; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '185; setting to 0 instead 673s Warning: skipping read '185' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '185' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '189; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '190; setting to 0 instead 673s Warning: skipping read '190' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '190' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '191; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '192; setting to 0 instead 673s Warning: skipping read '192' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '192' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '193; setting to 0 instead 673s Warning: skipping read '193' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '193' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '194; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '195; setting to 0 instead 673s Warning: skipping read '195' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '195' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '196; setting to 0 instead 673s 196 reads; of these: 673s 196 (100.00%) were unpaired; of these: 673s 180 (91.84%) aligned 0 times 673s 10 (5.10%) aligned exactly 1 time 673s 6 (3.06%) aligned >1 times 673s 8.16% overall alignment rate 673s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 673s Flattened IUPAC characters 673s Mutating sequence Sim.pm.1 673s Introducing 12 SNPs, 1/3 ref/read gaps, and 0 rearrangements 673s Finished SNPs 673s Finished ref gaps 673s Finished read gaps 673s Mutating sequence Sim.pm.2 673s Introducing 8 SNPs, 1/2 ref/read gaps, and 0 rearrangements 673s Finished SNPs 673s Finished ref gaps 673s Finished read gaps 673s Mutated reference genome to subject genome 673s SNPs introduced: 20 673s Reference gaps introduced: 2 673s Read gaps introduced: 5 673s Rearrangements introduced: 0 673s Created read sampler 673s Sampling 97 reads 673s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 673s *** Run 56 of 100 673s /usr/bin/bowtie2 --np 2 --cp-min 11 --score-min L,6.35733734414618,3.17890293952392 -R 1 --rdg 47.993499534413,18.0362209692033 -M 3 --trim5 8 --local --cp-ival 3 --nofw -i L,0.0207795813988263 --rfg 26.1155810332039,8.06299005372178 -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw 673s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 673s parsing sequence Sim.pm.1... 673s parsing sequence Sim.pm.2... 673s Parsed 143 reference bases 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '1' because it was < 2 characters long 673s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '2' because it was < 2 characters long 673s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '3' because it was < 2 characters long 673s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '7' because it was < 2 characters long 673s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '15' because it was < 2 characters long 673s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '17' because it was < 2 characters long 673s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '18' because it was < 2 characters long 673s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '19' because it was < 2 characters long 673s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '20' because it was < 2 characters long 673s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '22' because it was < 2 characters long 673s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '24' because it was < 2 characters long 673s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '25' because it was < 2 characters long 673s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '27' because it was < 2 characters long 673s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '32' because it was < 2 characters long 673s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '34' because it was < 2 characters long 673s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '35' because it was < 2 characters long 673s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '41' because it was < 2 characters long 673s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '42' because it was < 2 characters long 673s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '45' because it was < 2 characters long 673s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '46' because it was < 2 characters long 673s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '47' because it was < 2 characters long 673s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '54' because it was < 2 characters long 673s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '62' because it was < 2 characters long 673s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '63' because it was < 2 characters long 673s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '69' because it was < 2 characters long 673s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '76' because it was < 2 characters long 673s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '78' because it was < 2 characters long 673s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '84' because it was < 2 characters long 673s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '86' because it was < 2 characters long 673s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '87' because it was < 2 characters long 673s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '89' because it was < 2 characters long 673s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '90' because it was < 2 characters long 673s 97 reads; of these: 673s 97 (100.00%) were unpaired; of these: 673s 97 (100.00%) aligned 0 times 673s 0 (0.00%) aligned exactly 1 time 673s 0 (0.00%) aligned >1 times 673s 0.00% overall alignment rate 673s Read 50 alignments... 673s Read 100 alignments... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s --- Summary --- 673s Read 1 reference strings 673s Checked 0 alignments, 0 edits 673s --------------- 673s PASSED 673s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 673s /usr/bin/bowtie2 --np 2 --cp-min 11 --score-min L,6.35733734414618,3.17890293952392 -R 1 --rdg 47.993499534413,18.0362209692033 -M 3 --trim5 8 --local --cp-ival 3 --nofw -i L,0.0207795813988263 --rfg 26.1155810332039,8.06299005372178 -r -p 2 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '1' because it was < 2 characters long 673s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '2' because it was < 2 characters long 673s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '3' because it was < 2 characters long 673s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '7' because it was < 2 characters long 673s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '15' because it was < 2 characters long 673s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '17' because it was < 2 characters long 673s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '18' because it was < 2 characters long 673s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '19' because it was < 2 characters long 673s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '20' because it was < 2 characters long 673s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '22' because it was < 2 characters long 673s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '24' because it was < 2 characters long 673s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '25' because it was < 2 characters long 673s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '27' because it was < 2 characters long 673s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '32' because it was < 2 characters long 673s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '34' because it was < 2 characters long 673s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '35' because it was < 2 characters long 673s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '41' because it was < 2 characters long 673s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '42' because it was < 2 characters long 673s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '45' because it was < 2 characters long 673s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '46' because it was < 2 characters long 673s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '47' because it was < 2 characters long 673s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '54' because it was < 2 characters long 673s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '62' because it was < 2 characters long 673s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '63' because it was < 2 characters long 673s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '69' because it was < 2 characters long 673s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '76' because it was < 2 characters long 673s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '78' because it was < 2 characters long 673s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '84' because it was < 2 characters long 673s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '86' because it was < 2 characters long 673s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '87' because it was < 2 characters long 673s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '89' because it was < 2 characters long 673s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 673s Warning: skipping read '90' because it was < 2 characters long 673s 97 reads; of these: 673s 97 (100.00%) were unpaired; of these: 673s 97 (100.00%) aligned 0 times 673s 0 (0.00%) aligned exactly 1 time 673s 0 (0.00%) aligned >1 times 673s 0.00% overall alignment rate 673s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 673s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 673s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 673s Flattened IUPAC characters 673s Mutating sequence Sim.pm.1 673s Introducing 16 SNPs, 0/2 ref/read gaps, and 0 rearrangements 673s Finished SNPs 673s Finished ref gaps 673s Finished read gaps 673s Mutating sequence Sim.pm.2 673s Introducing 14 SNPs, 0/1 ref/read gaps, and 1 rearrangements 673s Finished SNPs 673s Finished ref gaps 673s Finished read gaps 673s Mutated reference genome to subject genome 673s SNPs introduced: 30 673s Reference gaps introduced: 0 673s Read gaps introduced: 3 673s Rearrangements introduced: 1 673s Created read sampler 673s Sampling 127 reads 673s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 673s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 673s parsing sequence Sim.pm.1... 673s parsing sequence Sim.pm.2... 673s Parsed 143 reference bases 673s *** Run 57 of 100 673s /usr/bin/bowtie2 --rfg 45.8214385867223 --rdg 24.667454957838,3.05742663791462 --mp 8.95254288938183,1.63640640447593 -k 2 --score-min L,3.06476800539777,7.57448346765297 --cp-ival 1 --trim5 0 --n-ceil 0.457362075278431,0.704599028868097 --cp-min 5 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 673s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 673s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '25' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 673s 127 reads; of these: 673s 127 (100.00%) were unpaired; of these: 673s 107 (84.25%) aligned 0 times 673s 11 (8.66%) aligned exactly 1 time 673s 9 (7.09%) aligned >1 times 673s 15.75% overall alignment rate 673s Read 50 alignments... 673s Read 100 alignments... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGA 673s GGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGA 673s Processing line... 673s AGGGAGCT 673s AGGGAGCT 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GTCA 673s GTCA 673s Processing line... 673s TGAC 673s TGAC 673s Processing line... 673s AGAGGCG 673s AGAGGCG 673s Processing line... 673s AGAGGCG 673s AGAGGCG 673s Processing line... 673s AGCTG 673s AGCTG 673s Processing line... 673s CAGCT 673s CAGCT 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GAG 673s GAG 673s Processing line... 673s GAG 673s GAG 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GTCTGCGCCCAGC 673s GTCTGCGCCCAGC 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GT 673s GT 673s Processing line... 673s GT 673s GT 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GGT 673s GGT 673s Processing line... 673s GGT 673s GGT 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s GTCAGGAGGGAGCTG 673s GTCAGGAGGGAGCTG 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s AGGG 673s AGGG 673s Processing line... 673s AGGG 673s AGGG 673s Processing line... 673s Processing line... 673s Processing line... 673s AGGGTG 673s AGGGTG 673s Processing line... 673s GAA 673s GAA 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s TAGGCGGTCAG 673s TAGGCGGTCAG 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s TCCGGGTGGTGTTGA 673s TCCGGGTGGTGTTGA 673s Processing line... 673s TCCGGGTGGTGTTGA 673s TCCGGGTGGTGTTGA 673s Processing line... 673s Processing line... 673s Processing line... 673s GAGGGTGACAGAGGCGT 673s GAGGGTGACAGAGGCGT 673s Processing line... 673s CCCAGCTTAGGCGGT 673s CCCAGCTTAGGCGGT 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s CC 673s CC 673s Processing line... 673s CC 673s CC 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s Processing line... 673s AGAGGGTGA 673s AGAGGGTGA 673s Processing line... 673s Processing line... 673s Processing line... 673s GGTGACA 673s GGTGACA 673s Processing line... 673s Processing line... 673s Processing line... 673s --- Summary --- 673s Read 1 reference strings 673s Checked 29 alignments, 0 edits 673s --------------- 673s PASSED 673s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 673s /usr/bin/bowtie2 --rfg 45.8214385867223 --rdg 24.667454957838,3.05742663791462 --mp 8.95254288938183,1.63640640447593 -k 2 --score-min L,3.06476800539777,7.57448346765297 --cp-ival 1 --trim5 0 --n-ceil 0.457362075278431,0.704599028868097 --cp-min 5 -f -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 673s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 673s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 673s Warning: skipping read '25' because it was < 2 characters long 673s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 673s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 674s 127 reads; of these: 674s 127 (100.00%) were unpaired; of these: 674s 107 (84.25%) aligned 0 times 674s 11 (8.66%) aligned exactly 1 time 674s 9 (7.09%) aligned >1 times 674s 15.75% overall alignment rate 674s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 674s Flattened IUPAC characters 674s Mutating sequence Sim.pm.1 674s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 674s Finished SNPs 674s Finished ref gaps 674s Finished read gaps 674s Mutating sequence Sim.pm.2 674s Introducing 5 SNPs, 1/3 ref/read gaps, and 2 rearrangements 674s Finished SNPs 674s Finished ref gaps 674s Finished read gaps 674s Mutated reference genome to subject genome 674s SNPs introduced: 8 674s Reference gaps introduced: 1 674s Read gaps introduced: 4 674s Rearrangements introduced: 2 674s Created read sampler 674s Sampling 36 reads 674s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 674s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 674s parsing sequence Sim.pm.1... 674s parsing sequence Sim.pm.2... 674s Parsed 143 reference bases 674s *** Run 58 of 100 674s /usr/bin/bowtie2 --rdg 17.9931221550402 --nofw --score-min L,4.51484599093064,8.26085997706889 --local --cp-ival 2 --cp-min 2 -M 4 --trim5 6 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 674s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 674s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read '5' because it was < 2 characters long 674s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '7' because it was < 2 characters long 674s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '8' because it was < 2 characters long 674s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '10' because it was < 2 characters long 674s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read '13' because it was < 2 characters long 674s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '26' because it was < 2 characters long 674s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '28' because it was < 2 characters long 674s 36 reads; of these: 674s 33 (91.67%) were paired; of these: 674s 33 (100.00%) aligned concordantly 0 times 674s 0 (0.00%) aligned concordantly exactly 1 time 674s 0 (0.00%) aligned concordantly >1 times 674s ---- 674s 33 pairs aligned concordantly 0 times; of these: 674s 0 (0.00%) aligned discordantly 1 time 674s ---- 674s 33 pairs aligned 0 times concordantly or discordantly; of these: 674s 66 mates make up the pairs; of these: 674s 66 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 3 (8.33%) were unpaired; of these: 674s 3 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 0.00% overall alignment rate 674s Read 50 alignments... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s --- Summary --- 674s Read 1 reference strings 674s Checked 0 alignments, 0 edits 674s --------------- 674s PASSED 674s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 674s /usr/bin/bowtie2 --rdg 17.9931221550402 --nofw --score-min L,4.51484599093064,8.26085997706889 --local --cp-ival 2 --cp-min 2 -M 4 --trim5 6 -r -p 4 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 674s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 674s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read '5' because it was < 2 characters long 674s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '7' because it was < 2 characters long 674s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '8' because it was < 2 characters long 674s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '10' because it was < 2 characters long 674s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read '13' because it was < 2 characters long 674s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '26' because it was < 2 characters long 674s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '28' because it was < 2 characters long 674s 36 reads; of these: 674s 33 (91.67%) were paired; of these: 674s 33 (100.00%) aligned concordantly 0 times 674s 0 (0.00%) aligned concordantly exactly 1 time 674s 0 (0.00%) aligned concordantly >1 times 674s ---- 674s 33 pairs aligned concordantly 0 times; of these: 674s 0 (0.00%) aligned discordantly 1 time 674s ---- 674s 33 pairs aligned 0 times concordantly or discordantly; of these: 674s 66 mates make up the pairs; of these: 674s 66 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 3 (8.33%) were unpaired; of these: 674s 3 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 0.00% overall alignment rate 674s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 674s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 674s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 674s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 674s /usr/bin/bowtie2 --rdg 17.9931221550402 --nofw --score-min L,4.51484599093064,8.26085997706889 --local --cp-ival 2 --cp-min 2 -M 4 --trim5 6 -r -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 674s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 674s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read '5' because it was < 2 characters long 674s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '7' because it was < 2 characters long 674s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '8' because it was < 2 characters long 674s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '10' because it was < 2 characters long 674s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read '13' because it was < 2 characters long 674s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '26' because it was < 2 characters long 674s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read '28' because it was < 2 characters long 674s 36 reads; of these: 674s 33 (91.67%) were paired; of these: 674s 33 (100.00%) aligned concordantly 0 times 674s 0 (0.00%) aligned concordantly exactly 1 time 674s 0 (0.00%) aligned concordantly >1 times 674s ---- 674s 33 pairs aligned concordantly 0 times; of these: 674s 0 (0.00%) aligned discordantly 1 time 674s ---- 674s 33 pairs aligned 0 times concordantly or discordantly; of these: 674s 66 mates make up the pairs; of these: 674s 66 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 3 (8.33%) were unpaired; of these: 674s 3 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 0.00% overall alignment rate 674s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 674s Flattened IUPAC characters 674s Mutating sequence Sim.pm.1 674s Introducing 12 SNPs, 0/1 ref/read gaps, and 2 rearrangements 674s Finished SNPs 674s Finished ref gaps 674s Finished read gaps 674s Mutating sequence Sim.pm.2 674s Introducing 15 SNPs, 4/2 ref/read gaps, and 0 rearrangements 674s Finished SNPs 674s Finished ref gaps 674s Finished read gaps 674s Mutated reference genome to subject genome 674s SNPs introduced: 27 674s Reference gaps introduced: 4 674s Read gaps introduced: 3 674s Rearrangements introduced: 2 674s Created read sampler 674s Sampling 52 reads 674s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 674s *** Run 59 of 100 674s /usr/bin/bowtie2 --cp-ival 1 --local --trim5 3 --norc --mp 6.08102540992534,1.90096814631591 --nofw --trim3 4 --cp-min 10 --np 4 --mm -R 4 -k 4 --score-min L,2.44252412189476,4.86787958339311 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 674s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 674s parsing sequence Sim.pm.1... 674s parsing sequence Sim.pm.2... 674s Parsed 143 reference bases 674s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 674s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 674s Warning: skipping mate #2 of read 'R_1_1_1_41_41_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 674s 52 reads; of these: 674s 45 (86.54%) were paired; of these: 674s 45 (100.00%) aligned concordantly 0 times 674s 0 (0.00%) aligned concordantly exactly 1 time 674s 0 (0.00%) aligned concordantly >1 times 674s ---- 674s 45 pairs aligned concordantly 0 times; of these: 674s 0 (0.00%) aligned discordantly 1 time 674s ---- 674s 45 pairs aligned 0 times concordantly or discordantly; of these: 674s 90 mates make up the pairs; of these: 674s 90 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 7 (13.46%) were unpaired; of these: 674s 7 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 0.00% overall alignment rate 674s Read 50 alignments... 674s Read 100 alignments... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s /usr/bin/bowtie2 --cp-ival 1 --local --trim5 3 --norc --mp 6.08102540992534,1.90096814631591 --nofw --trim3 4 --cp-min 10 --np 4 --mm -R 4 -k 4 --score-min L,2.44252412189476,4.86787958339311 --qseq -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s --- Summary --- 674s Read 1 reference strings 674s Checked 0 alignments, 0 edits 674s --------------- 674s PASSED 674s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 674s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 674s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 674s Warning: skipping mate #2 of read 'R_1_1_1_41_41_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 674s 52 reads; of these: 674s 45 (86.54%) were paired; of these: 674s 45 (100.00%) aligned concordantly 0 times 674s 0 (0.00%) aligned concordantly exactly 1 time 674s 0 (0.00%) aligned concordantly >1 times 674s ---- 674s 45 pairs aligned concordantly 0 times; of these: 674s 0 (0.00%) aligned discordantly 1 time 674s ---- 674s 45 pairs aligned 0 times concordantly or discordantly; of these: 674s 90 mates make up the pairs; of these: 674s 90 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 7 (13.46%) were unpaired; of these: 674s 7 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 0.00% overall alignment rate 674s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 674s Flattened IUPAC characters 674s Mutating sequence Sim.pm.1 674s Introducing 4 SNPs, 0/0 ref/read gaps, and 2 rearrangements 674s Finished SNPs 674s Finished ref gaps 674s Finished read gaps 674s *** Run 60 of 100 674s /usr/bin/bowtie2 --trim3 3 --mp 6.46277390762036,1.18412016129597 --local --cp-ival 1 --trim5 3 --mm --score-min L,7.87273337467683,5.66323032666677 -R 2 --cp-min 3 --np 2 --qseq -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.qseq 674s Mutating sequence Sim.pm.2 674s Introducing 8 SNPs, 1/1 ref/read gaps, and 0 rearrangements 674s Finished SNPs 674s Finished ref gaps 674s Finished read gaps 674s Mutated reference genome to subject genome 674s SNPs introduced: 12 674s Reference gaps introduced: 1 674s Read gaps introduced: 1 674s Rearrangements introduced: 2 674s Created read sampler 674s Sampling 70 reads 674s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 674s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 674s parsing sequence Sim.pm.1... 674s parsing sequence Sim.pm.2... 674s Parsed 143 reference bases 674s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 674s 70 reads; of these: 674s 70 (100.00%) were unpaired; of these: 674s 70 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 0.00% overall alignment rate 674s Read 50 alignments... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s --- Summary --- 674s Read 1 reference strings 674s Checked 0 alignments, 0 edits 674s --------------- 674s PASSED 674s Flattened IUPAC characters 674s Mutating sequence Sim.pm.1 674s Introducing 4 SNPs, 2/2 ref/read gaps, and 0 rearrangements 674s Finished SNPs 674s Finished ref gaps 674s Finished read gaps 674s Mutating sequence Sim.pm.2 674s Introducing 12 SNPs, 2/1 ref/read gaps, and 3 rearrangements 674s Finished SNPs 674s Finished ref gaps 674s Finished read gaps 674s Mutated reference genome to subject genome 674s SNPs introduced: 16 674s Reference gaps introduced: 4 674s Read gaps introduced: 3 674s Rearrangements introduced: 3 674s Created read sampler 674s Sampling 191 reads 674s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 674s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 674s parsing sequence Sim.pm.1... 674s parsing sequence Sim.pm.2... 674s Parsed 143 reference bases 674s *** Run 61 of 100 674s /usr/bin/bowtie2 --np 2 --cp-min 9 --rdg 16.5088463980946 --score-min L,9.38210296746285,4.14531806965919 --local --cp-ival 1 -M 4 --norc --nofw --trim3 3 --mp 2.3445355628084,1.03406619741378 -i S,2.4268919524205 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 674s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 674s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 674s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 674s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 674s Warning: skipping mate #2 of read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 674s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 674s Read 50 alignments... 674s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 674s Warning: skipping mate #2 of read 'R_1_1_1_127_127_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 674s Read 100 alignments... 674s Read 150 alignments... 674s Read 200 alignments... 674s Read 250 alignments... 674s Warning: skipping mate #2 of read 'R_1_1_1_165_165_1/1' because length (1) <= # seed mismatches (0) 674s Warning: skipping mate #2 of read 'R_1_1_1_165_165_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_168_168_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 674s Warning: skipping read 'R_1_1_1_173_173_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping read 'R_1_1_1_173_173_1/1' because it was < 2 characters long 674s Warning: skipping mate #1 of read 'R_1_1_1_179_179_1/1' because length (0) <= # seed mismatches (0) 674s Warning: skipping mate #1 of read 'R_1_1_1_179_179_1/1' because it was < 2 characters long 674s 191 reads; of these: 674s 175 (91.62%) were paired; of these: 674s 175 (100.00%) aligned concordantly 0 times 674s 0 (0.00%) aligned concordantly exactly 1 time 674s 0 (0.00%) aligned concordantly >1 times 674s ---- 674s 175 pairs aligned concordantly 0 times; of these: 674s 0 (0.00%) aligned discordantly 1 time 674s ---- 674s 175 pairs aligned 0 times concordantly or discordantly; of these: 674s 350 mates make up the pairs; of these: 674s 350 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 16 (8.38%) were unpaired; of these: 674s 16 (100.00%) aligned 0 times 674s 0 (0.00%) aligned exactly 1 time 674s 0 (0.00%) aligned >1 times 674s 0.00% overall alignment rate 674s Read 300 alignments... 674s Read 350 alignments... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing 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line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s 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line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s Processing line... 674s --- Summary --- 674s Read 1 reference strings 674s Checked 0 alignments, 0 edits 674s --------------- 674s PASSED 674s Flattened IUPAC characters 674s Mutating sequence Sim.pm.2 674s Introducing 0 SNPs, 0/0 ref/read gaps, and 2 rearrangements 674s Finished SNPs 674s Finished ref gaps 674s Finished read gaps 674s Mutating sequence Sim.pm.1 674s Introducing 14 SNPs, 2/1 ref/read gaps, and 0 rearrangements 674s Finished SNPs 674s Finished ref gaps 674s Finished read gaps 674s Mutated reference genome to subject genome 674s SNPs introduced: 14 674s Reference gaps introduced: 2 674s Read gaps introduced: 1 674s Rearrangements introduced: 2 674s Created read sampler 674s Sampling 60 reads 674s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 674s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 674s parsing sequence Sim.pm.1... 674s parsing sequence Sim.pm.2... 674s Parsed 143 reference bases 674s *** Run 62 of 100 674s /usr/bin/bowtie2 --np 3 --cp-min 2 --trim5 4 --cp-ival 1 --ma 29.3770052911925 --trim3 1 --score-min L,6.76003558403022,7.52348678489047 -D 10 -k 2 -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw 675s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 675s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 675s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '0' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 675s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 675s Warning: skipping read '11' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 675s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 675s Warning: skipping read '15' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 675s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '16' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 675s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 675s Warning: skipping read '24' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 675s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 675s Warning: skipping read '33' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 675s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '42' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 675s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 675s Warning: skipping read '59' because it was < 2 characters long 675s 60 reads; of these: 675s 60 (100.00%) were unpaired; of these: 675s 38 (63.33%) aligned 0 times 675s 16 (26.67%) aligned exactly 1 time 675s 6 (10.00%) aligned >1 times 675s 36.67% overall alignment rate 675s Read 50 alignments... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s TTGAGA 675s TTGAGA 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s ACAG 675s ACAG 675s Processing line... 675s GGGACTGGCGGGAAGACCGCGGCTCGGTCTGCG 675s GGGACTGGCGGGAAGACCGCGGCTCGGTCTGCG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GGTGGTGTTGAGA 675s GGTGGTGTTGAGA 675s Processing line... 675s Processing line... 675s Processing line... 675s GGAG 675s GGAG 675s Processing line... 675s GGAG 675s GGAG 675s Processing line... 675s Processing line... 675s Processing line... 675s CTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGG 675s CTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGG 675s Processing line... 675s ACTG 675s ACTG 675s Processing line... 675s TGGTGTTGA 675s TGGTGTTGA 675s Processing line... 675s TGGTGTTGA 675s TGGTGTTGA 675s Processing line... 675s GGGACTG 675s GGGACTG 675s Processing line... 675s CGCCCAGCTTA 675s CGCCCAGCTTA 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s CCGGGTGG 675s CCGGGTGG 675s Processing line... 675s CCGGGTGG 675s CCGGGTGG 675s Processing line... 675s Processing line... 675s Processing line... 675s GCGCCCAGCTTAGGCGGTCAGGAGGGAGCTG 675s GCGCCCAGCTTAGGCGGTCAGGAGGGAGCTG 675s Processing line... 675s GACCGCGGCTCGGTCT 675s GACCGCGGCTCGGTCT 675s Processing line... 675s Processing line... 675s Processing line... 675s CAGGA 675s CAGGA 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s TAGGGGGGGACTGGCGGGAAGACCGCGGCTC 675s TAGGGGGGGACTGGCGGGAAGACCGCGGCTC 675s Processing line... 675s CGGGAAGACCGCGGC 675s CGGGAAGACCGCGGC 675s Processing line... 675s TTAGGCGG 675s TTAGGCGG 675s Processing line... 675s Processing line... 675s GGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCA 675s GGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCA 675s Processing line... 675s CTG 675s CTG 675s Processing line... 675s CTG 675s CTG 675s Processing line... 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GGCG 675s GGCG 675s Processing line... 675s CGCC 675s CGCC 675s Processing line... 675s GGGAAGACCGCGGCTCGGTCTGCGCCCAG 675s GGGAAGACCGCGGCTCGGTCTGCGCCCAG 675s Processing line... 675s Processing line... 675s --- Summary --- 675s Read 1 reference strings 675s Checked 28 alignments, 0 edits 675s --------------- 675s PASSED 675s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 675s /usr/bin/bowtie2 --np 3 --cp-min 2 --trim5 4 --cp-ival 1 --ma 29.3770052911925 --trim3 1 --score-min L,6.76003558403022,7.52348678489047 -D 10 -k 2 -r -p 4 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 675s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 675s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 675s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '0' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 675s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 675s Warning: skipping read '11' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 675s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 675s Warning: skipping read '15' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 675s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '16' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 675s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 675s Warning: skipping read '24' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 675s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 675s Warning: skipping read '33' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 675s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '42' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 675s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 675s Warning: skipping read '59' because it was < 2 characters long 675s 60 reads; of these: 675s 60 (100.00%) were unpaired; of these: 675s 38 (63.33%) aligned 0 times 675s 16 (26.67%) aligned exactly 1 time 675s 6 (10.00%) aligned >1 times 675s 36.67% overall alignment rate 675s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 675s Flattened IUPAC characters 675s Mutating sequence Sim.pm.2 675s Introducing 0 SNPs, 0/2 ref/read gaps, and 0 rearrangements 675s Finished SNPs 675s Finished ref gaps 675s Finished read gaps 675s Mutating sequence Sim.pm.1 675s Introducing 14 SNPs, 0/1 ref/read gaps, and 2 rearrangements 675s Finished SNPs 675s Finished ref gaps 675s Finished read gaps 675s Mutated reference genome to subject genome 675s SNPs introduced: 14 675s Reference gaps introduced: 0 675s Read gaps introduced: 3 675s Rearrangements introduced: 2 675s Created read sampler 675s Sampling 128 reads 675s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 675s *** Run 63 of 100 675s /usr/bin/bowtie2 --mm --rdg 26.4568629753 -D 5 -k 3 --score-min L,1.78616469671205,4.8914054575234 --nofw --cp-ival 1 --trim5 2 --cp-min 5 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 675s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 675s parsing sequence Sim.pm.1... 675s parsing sequence Sim.pm.2... 675s Parsed 143 reference bases 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 675s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '15' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 675s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '23' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 675s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 675s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '29' because it was < 2 characters long 675s Warning: skipping mate #2 of read '29' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 675s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '33' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 675s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '38' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 675s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 675s Warning: skipping mate #2 of read '40' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 675s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '46' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 675s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 675s Warning: skipping mate #2 of read '63' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 675s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 675s Warning: skipping mate #2 of read '82' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 675s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '91' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 675s Read 50 alignments... 675s Read 100 alignments... 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 675s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '112' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 675s Read 150 alignments... 675s Read 200 alignments... 675s 128 reads; of these: 675s 121 (94.53%) were paired; of these: 675s 119 (98.35%) aligned concordantly 0 times 675s 0 (0.00%) aligned concordantly exactly 1 time 675s 2 (1.65%) aligned concordantly >1 times 675s ---- 675s 119 pairs aligned concordantly 0 times; of these: 675s 4 (3.36%) aligned discordantly 1 time 675s ---- 675s 115 pairs aligned 0 times concordantly or discordantly; of these: 675s 230 mates make up the pairs; of these: 675s 207 (90.00%) aligned 0 times 675s 11 (4.78%) aligned exactly 1 time 675s 12 (5.22%) aligned >1 times 675s 7 (5.47%) were unpaired; of these: 675s 7 (100.00%) aligned 0 times 675s 0 (0.00%) aligned exactly 1 time 675s 0 (0.00%) aligned >1 times 675s 14.06% overall alignment rate 675s Read 250 alignments... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s TGGCGGGAA 675s TGGCGGGAA 675s Processing line... 675s Processing line... 675s GT 675s GT 675s Processing line... 675s GT 675s GT 675s Processing line... 675s GT 675s GT 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GGGACT 675s GGGACT 675s Processing line... 675s Processing line... 675s GGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGA 675s GGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGA 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGC 675s GGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGC 675s Processing line... 675s Processing line... 675s Processing line... 675s GTG 675s GTG 675s Processing line... 675s GTG 675s GTG 675s Processing line... 675s GTG 675s GTG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s AGG 675s AGG 675s Processing line... 675s AGG 675s AGG 675s Processing line... 675s AGG 675s AGG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s TGGTG 675s TGGTG 675s Processing line... 675s TGGTG 675s TGGTG 675s Processing line... 675s TGGTG 675s TGGTG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s CCG 675s CCG 675s Processing line... 675s CCG 675s CCG 675s Processing line... 675s CCG 675s CCG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s ACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTA 675s ACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTA 675s Processing line... 675s AGGCGGTCAGGAGGG 675s AGGCGGTCAGGAGGG 675s Processing line... 675s Processing line... 675s Processing line... 675s TG 675s TG 675s Processing line... 675s TG 675s TG 675s Processing line... 675s TG 675s TG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGC 675s GGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GTGTTG 675s GTGTTG 675s Processing line... 675s TGA 675s TGA 675s Processing line... 675s GTGTTG 675s GTGTTG 675s Processing line... 675s TGA 675s TGA 675s Processing line... 675s Processing line... 675s Processing line... 675s GT 675s GT 675s Processing line... 675s GCTCGGTCTGCGCCCAGCTTAGGC 675s GCTCGGTCTGCGCCCAGCTTAGGC 675s Processing line... 675s GGTCTGCGCCCAGCTTAGGCGGTCAGGAG 675s GGTCTGCGCCCAGCTTAGGCGGTCAGGAG 675s Processing line... 675s AGCT 675s AGCT 675s Processing line... 675s AGCT 675s AGCT 675s Processing line... 675s Processing line... 675s Processing line... 675s CA 675s CA 675s Processing line... 675s CA 675s CA 675s Processing line... 675s CA 675s CA 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s CCC 675s CCC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s CGGCTCGGTCTGCG 675s CGGCTCGGTCTGCG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GTTGAGAGGGT 675s GTTGAGAGGGT 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s TC 675s TC 675s Processing line... 675s TC 675s TC 675s Processing line... 675s TC 675s TC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s CTCGGTCTG 675s CTCGGTCTG 675s Processing line... 675s GGCGGTCAGGAGGGAG 675s GGCGGTCAGGAGGGAG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GTGGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAG 675s GTGGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAG 675s Processing line... 675s Processing line... 675s TG 675s TG 675s Processing line... 675s TG 675s TG 675s Processing line... 675s TG 675s TG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GACTGGCGGGAAGAC 675s GACTGGCGGGAAGAC 675s Processing line... 675s GCTTAGGCGGTCAGGAGGGAGC 675s GCTTAGGCGGTCAGGAGGGAGC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GAAGACCGCGGCTCGGTC 675s GAAGACCGCGGCTCGGTC 675s Processing line... 675s GGAGGGAGCTGG 675s GGAGGGAGCTGG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GC 675s GC 675s Processing line... 675s GC 675s GC 675s Processing line... 675s GC 675s GC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GCGGCTCGGTCTGC 675s GCGGCTCGGTCTGC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s --- Summary --- 675s Read 1 reference strings 675s Checked 60 alignments, 0 edits 675s --------------- 675s PASSED 675s ALSO checking that bowtie2 and bowtie2-align match up 675s /usr/bin/bowtie2 --mm --rdg 26.4568629753 -D 5 -k 3 --score-min L,1.78616469671205,4.8914054575234 --nofw --cp-ival 1 --trim5 2 --cp-min 5 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 675s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '15' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 675s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '23' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 675s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 675s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '29' because it was < 2 characters long 675s Warning: skipping mate #2 of read '29' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 675s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '33' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 675s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '38' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 675s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 675s Warning: skipping mate #2 of read '40' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 675s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '46' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 675s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 675s Warning: skipping mate #2 of read '63' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 675s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 675s Warning: skipping mate #2 of read '82' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 675s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '91' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 675s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 675s Warning: skipping mate #1 of read '112' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 675s 128 reads; of these: 675s 121 (94.53%) were paired; of these: 675s 119 (98.35%) aligned concordantly 0 times 675s 0 (0.00%) aligned concordantly exactly 1 time 675s 2 (1.65%) aligned concordantly >1 times 675s ---- 675s 119 pairs aligned concordantly 0 times; of these: 675s 4 (3.36%) aligned discordantly 1 time 675s ---- 675s 115 pairs aligned 0 times concordantly or discordantly; of these: 675s 230 mates make up the pairs; of these: 675s 207 (90.00%) aligned 0 times 675s 11 (4.78%) aligned exactly 1 time 675s 12 (5.22%) aligned >1 times 675s 7 (5.47%) were unpaired; of these: 675s 7 (100.00%) aligned 0 times 675s 0 (0.00%) aligned exactly 1 time 675s 0 (0.00%) aligned >1 times 675s 14.06% overall alignment rate 675s Flattened IUPAC characters 675s Mutating sequence Sim.pm.1 675s Introducing 12 SNPs, 0/1 ref/read gaps, and 0 rearrangements 675s Finished SNPs 675s Finished ref gaps 675s Finished read gaps 675s Mutating sequence Sim.pm.2 675s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 675s Finished SNPs 675s Finished ref gaps 675s Finished read gaps 675s Mutated reference genome to subject genome 675s SNPs introduced: 18 675s Reference gaps introduced: 0 675s Read gaps introduced: 1 675s Rearrangements introduced: 1 675s Created read sampler 675s Sampling 145 reads 675s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 675s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 675s parsing sequence Sim.pm.1... 675s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 675s parsing sequence Sim.pm.2... 675s Parsed 143 reference bases 675s *** Run 64 of 100 675s /usr/bin/bowtie2 --cp-ival 3 --np 1 --cp-min 4 -a --rfg 30.6162707751538 -N 1 -L21 -D 3 --trim3 7 --score-min L,1.25927020843977,7.21937205160345 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 675s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 675s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '4' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 675s Warning: skipping read '10' because length (1) <= # seed mismatches (1) 675s Warning: skipping read '10' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 675s Warning: skipping read '11' because length (1) <= # seed mismatches (1) 675s Warning: skipping read '11' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 675s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '16' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 675s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '22' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 675s Warning: skipping read '26' because length (1) <= # seed mismatches (1) 675s Warning: skipping read '26' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 675s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '32' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 675s Warning: skipping read '45' because length (1) <= # seed mismatches (1) 675s Warning: skipping read '45' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 675s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '48' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 675s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '51' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 675s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '52' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 675s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '55' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 675s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '62' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 675s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '63' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 675s Warning: skipping read '65' because length (1) <= # seed mismatches (1) 675s Warning: skipping read '65' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 675s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '68' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 675s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '75' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 675s Warning: skipping read '77' because length (1) <= # seed mismatches (1) 675s Warning: skipping read '77' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 675s Warning: skipping read '85' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '85' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 675s Warning: skipping read '94' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '94' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 675s Warning: skipping read '95' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '95' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 675s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '99' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 675s Warning: skipping read '107' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '107' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 675s Warning: skipping read '112' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '112' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 675s Warning: skipping read '115' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '115' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 675s Warning: skipping read '118' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '118' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 675s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '125' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 675s Warning: skipping read '129' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '129' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 675s Warning: skipping read '131' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '131' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 675s Warning: skipping read '141' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '141' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 675s Warning: skipping read '145' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '145' because it was < 2 characters long 675s Read 50 alignments... 675s 145 reads; of these: 675s 145 (100.00%) were unpaired; of these: 675s 121 (83.45%) aligned 0 times 675s 16 (11.03%) aligned exactly 1 time 675s 8 (5.52%) aligned >1 times 675s 16.55% overall alignment rate 675s Read 100 alignments... 675s Read 150 alignments... 675s Read 200 alignments... 675s Read 250 alignments... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GAG 675s GAG 675s Processing line... 675s GAG 675s GAG 675s Processing line... 675s GAG 675s GAG 675s Processing line... 675s CTC 675s CTC 675s Processing line... 675s GAG 675s GAG 675s Processing line... 675s GAG 675s GAG 675s Processing line... 675s GAG 675s GAG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s ACCGCGGCTC 675s ACCGCGGCTC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GCGGCTCGGT 675s GCGGCTCGGT 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s AGACCGCGGCTCGG 675s AGACCGCGGCTCGG 675s Processing line... 675s ACAGAGGCG 675s ACAGAGGCG 675s Processing line... 675s Processing line... 675s CTGGCGG 675s CTGGCGG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GGAAGACCGCGGCTCGGTCTGCGC 675s GGAAGACCGCGGCTCGGTCTGCGC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s ACCGCGGCTC 675s ACCGCGGCTC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s CTG 675s CTG 675s Processing line... 675s CTG 675s CTG 675s Processing line... 675s CTG 675s CTG 675s Processing line... 675s CAG 675s CAG 675s Processing line... 675s CAG 675s CAG 675s Processing line... 675s CTG 675s CTG 675s Processing line... 675s CAG 675s CAG 675s Processing line... 675s Processing line... 675s TGGTGTTGAGAGGGTGA 675s TGGTGTTGAGAGGGTGA 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GTTGAGAGG 675s GTTGAGAGG 675s Processing line... 675s Processing line... 675s Processing line... 675s AAGACCGCGGCTCGGTCTGCGCC 675s AAGACCGCGGCTCGGTCTGCGCC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s CCGGGTGGTGTT 675s CCGGGTGGTGTT 675s Processing line... 675s CCGGGTGGTGTT 675s CCGGGTGGTGTT 675s Processing line... 675s Processing line... 675s GCGGCTCGGTCTGC 675s GCGGCTCGGTCTGC 675s Processing line... 675s GCTCGGTCTGCGC 675s GCTCGGTCTGCGC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s TTGAGA 675s TTGAGA 675s Processing line... 675s Processing line... 675s Processing line... 675s CCGGGT 675s CCGGGT 675s Processing line... 675s CCGGGT 675s CCGGGT 675s Processing line... 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s CC 675s CC 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s CC 675s CC 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s CC 675s CC 675s Processing line... 675s GG 675s GG 675s Processing line... 675s CC 675s CC 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s CC 675s CC 675s Processing line... 675s GG 675s GG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s CC 675s CC 675s Processing line... 675s CC 675s CC 675s Processing line... 675s CC 675s CC 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s CC 675s CC 675s Processing line... 675s GG 675s GG 675s Processing line... 675s CC 675s CC 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s AGACCGCGGCTCGGTCTGC 675s AGACCGCGGCTCGGTCTGC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GTGGT 675s GTGGT 675s Processing line... 675s GTGGT 675s GTGGT 675s Processing line... 675s GTGGT 675s GTGGT 675s Processing line... 675s GTGGT 675s GTGGT 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s CC 675s CC 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s CC 675s CC 675s Processing line... 675s CC 675s CC 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s CC 675s CC 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s GG 675s GG 675s Processing line... 675s CC 675s CC 675s Processing line... 675s GG 675s GG 675s Processing line... 675s Processing line... 675s Processing line... 675s GGCTCGGTCT 675s GGCTCGGTCT 675s Processing line... 675s CTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGC 675s CTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGC 675s Processing line... 675s --- Summary --- 675s Read 1 reference strings 675s Checked 149 alignments, 0 edits 675s --------------- 675s PASSED 675s ALSO checking that bowtie2 and bowtie2-align match up 675s /usr/bin/bowtie2 --cp-ival 3 --np 1 --cp-min 4 -a --rfg 30.6162707751538 -N 1 -L21 -D 3 --trim3 7 --score-min L,1.25927020843977,7.21937205160345 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 675s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 675s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '4' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 675s Warning: skipping read '10' because length (1) <= # seed mismatches (1) 675s Warning: skipping read '10' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 675s Warning: skipping read '11' because length (1) <= # seed mismatches (1) 675s Warning: skipping read '11' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 675s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '16' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 675s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '22' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 675s Warning: skipping read '26' because length (1) <= # seed mismatches (1) 675s Warning: skipping read '26' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 675s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '32' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 675s Warning: skipping read '45' because length (1) <= # seed mismatches (1) 675s Warning: skipping read '45' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 675s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '48' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 675s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '51' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 675s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '52' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 675s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '55' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 675s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '62' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 675s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '63' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 675s Warning: skipping read '65' because length (1) <= # seed mismatches (1) 675s Warning: skipping read '65' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 675s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '68' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 675s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '75' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 675s Warning: skipping read '77' because length (1) <= # seed mismatches (1) 675s Warning: skipping read '77' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 675s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 675s *** Run 65 of 100 675s /usr/bin/bowtie2 -R 1 --score-min L,4.39304682445199,2.65196607653849 --trim3 4 -M 2 --cp-min 4 --cp-ival 1 -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw 675s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 675s Warning: skipping read '85' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '85' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 675s Warning: skipping read '94' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '94' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 675s Warning: skipping read '95' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '95' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 675s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '99' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 675s Warning: skipping read '107' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '107' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 675s Warning: skipping read '112' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '112' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 675s Warning: skipping read '115' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '115' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 675s Warning: skipping read '118' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '118' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 675s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '125' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 675s Warning: skipping read '129' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '129' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 675s Warning: skipping read '131' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '131' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 675s Warning: skipping read '141' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '141' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 675s Warning: skipping read '145' because length (0) <= # seed mismatches (1) 675s Warning: skipping read '145' because it was < 2 characters long 675s 145 reads; of these: 675s 145 (100.00%) were unpaired; of these: 675s 121 (83.45%) aligned 0 times 675s 16 (11.03%) aligned exactly 1 time 675s 8 (5.52%) aligned >1 times 675s 16.55% overall alignment rate 675s Flattened IUPAC characters 675s Mutating sequence Sim.pm.2 675s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 675s Finished SNPs 675s Finished ref gaps 675s Finished read gaps 675s Mutating sequence Sim.pm.1 675s Introducing 0 SNPs, 1/2 ref/read gaps, and 1 rearrangements 675s Finished SNPs 675s Finished ref gaps 675s Finished read gaps 675s Mutated reference genome to subject genome 675s SNPs introduced: 5 675s Reference gaps introduced: 1 675s Read gaps introduced: 2 675s Rearrangements introduced: 2 675s Created read sampler 675s Sampling 85 reads 675s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 675s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 675s parsing sequence Sim.pm.1... 675s parsing sequence Sim.pm.2... 675s Parsed 143 reference bases 675s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 675s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 675s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '3' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 675s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '14' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 675s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '15' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 675s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '36' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 675s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '48' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 675s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '59' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 675s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '64' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 675s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 675s Warning: skipping read '71' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 675s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '75' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 675s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '80' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 675s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '82' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 675s 85 reads; of these: 675s 85 (100.00%) were unpaired; of these: 675s 63 (74.12%) aligned 0 times 675s 12 (14.12%) aligned exactly 1 time 675s 10 (11.76%) aligned >1 times 675s 25.88% overall alignment rate 675s Read 50 alignments... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s CG 675s CG 675s Processing line... 675s Processing line... 675s GGTAGGGGG 675s GGTAGGGGG 675s Processing line... 675s GGTCTGC 675s GGTCTGC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GTGGTAG 675s GTGGTAG 675s Processing line... 675s TG 675s TG 675s Processing line... 675s AGAGGC 675s AGAGGC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GG 675s GG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GTCTGCGCCCAGCTT 675s GTCTGCGCCCAGCTT 675s Processing line... 675s Processing line... 675s GAGGGTGA 675s GAGGGTGA 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s CT 675s CT 675s Processing line... 675s Processing line... 675s CCCAGCTTAGGCGGTCAGGA 675s CCCAGCTTAGGCGGTCAGGA 675s Processing line... 675s Processing line... 675s Processing line... 675s TGG 675s TGG 675s Processing line... 675s GGGTGACAGAGGC 675s GGGTGACAGAGGC 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s AGGGAGCTG 675s AGGGAGCTG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s TGTTGA 675s TGTTGA 675s Processing line... 675s GG 675s GG 675s Processing line... 675s Processing line... 675s TCAGGAGGG 675s TCAGGAGGG 675s Processing line... 675s Processing line... 675s Processing line... 675s TGAGAGGGTGA 675s TGAGAGGGTGA 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GACTGGCGGGAAGACCGCGGCTCG 675s GACTGGCGGGAAGACCGCGGCTCG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GGC 675s GGC 675s Processing line... 675s Processing line... 675s Processing line... 675s GAGGCGTG 675s GAGGCGTG 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s Processing line... 675s GAAGACCGCGGCTCGGTCTGCGCCC 675s GAAGACCGCGGCTCGGTCTGCGCCC 675s Processing line... 675s Processing line... 675s Processing line... 675s --- Summary --- 675s Read 1 reference strings 675s Checked 22 alignments, 0 edits 675s --------------- 675s PASSED 675s ALSO checking that bowtie2 and bowtie2-align match up 675s /usr/bin/bowtie2 -R 1 --score-min L,4.39304682445199,2.65196607653849 --trim3 4 -M 2 --cp-min 4 --cp-ival 1 -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 675s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 675s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 675s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '3' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 675s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '14' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 675s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '15' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 675s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '36' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 675s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '48' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 675s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '59' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 675s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '64' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 675s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 675s Warning: skipping read '71' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 675s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '75' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 675s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '80' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 675s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 675s Warning: skipping read '82' because it was < 2 characters long 675s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 675s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 675s 85 reads; of these: 675s 85 (100.00%) were unpaired; of these: 675s 63 (74.12%) aligned 0 times 675s 12 (14.12%) aligned exactly 1 time 675s 10 (11.76%) aligned >1 times 675s 25.88% overall alignment rate 675s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 675s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 675s /usr/bin/bowtie2 -R 1 --score-min L,4.39304682445199,2.65196607653849 --trim3 4 -M 2 --cp-min 4 --cp-ival 1 -r -p 2 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 676s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 676s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 676s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '3' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 676s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '14' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 676s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '15' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 676s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '36' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 676s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '48' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 676s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '59' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 676s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '64' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 676s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 676s Warning: skipping read '71' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 676s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '75' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 676s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '80' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 676s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '82' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 676s 85 reads; of these: 676s 85 (100.00%) were unpaired; of these: 676s 63 (74.12%) aligned 0 times 676s 12 (14.12%) aligned exactly 1 time 676s 10 (11.76%) aligned >1 times 676s 25.88% overall alignment rate 676s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 676s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 676s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 676s Flattened IUPAC characters 676s Mutating sequence Sim.pm.2 676s Introducing 11 SNPs, 0/0 ref/read gaps, and 0 rearrangements 676s Finished SNPs 676s Finished ref gaps 676s Finished read gaps 676s Mutating sequence Sim.pm.1 676s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 676s Finished SNPs 676s Finished ref gaps 676s Finished read gaps 676s Mutated reference genome to subject genome 676s SNPs introduced: 17 676s Reference gaps introduced: 0 676s Read gaps introduced: 0 676s Rearrangements introduced: 0 676s Created read sampler 676s Sampling 33 reads 676s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 676s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 676s parsing sequence Sim.pm.1... 676s parsing sequence Sim.pm.2... 676s Parsed 143 reference bases 676s *** Run 66 of 100 676s /usr/bin/bowtie2 --np 1 --cp-min 2 --rdg 28.4750311660476 --mm --score-min L,2.64955352582599,1.78754364975784 --cp-ival 2 --norc --trim3 2 --mp 8.02105962289035,2.39193168576536 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 676s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 676s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 676s 33 reads; of these: 676s 32 (96.97%) were paired; of these: 676s 31 (96.88%) aligned concordantly 0 times 676s 0 (0.00%) aligned concordantly exactly 1 time 676s 1 (3.12%) aligned concordantly >1 times 676s ---- 676s 31 pairs aligned concordantly 0 times; of these: 676s 0 (0.00%) aligned discordantly 1 time 676s ---- 676s 31 pairs aligned 0 times concordantly or discordantly; of these: 676s 62 mates make up the pairs; of these: 676s 55 (88.71%) aligned 0 times 676s 3 (4.84%) aligned exactly 1 time 676s 4 (6.45%) aligned >1 times 676s 1 (3.03%) were unpaired; of these: 676s 1 (100.00%) aligned 0 times 676s 0 (0.00%) aligned exactly 1 time 676s 0 (0.00%) aligned >1 times 676s 13.85% overall alignment rate 676s Read 50 alignments... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s CCC 676s CCC 676s Processing line... 676s Processing line... 676s GTGGT 676s GTGGT 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s GAGAGGGTGACAGAGGCGTG 676s GAGAGGGTGACAGAGGCGTG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s /usr/bin/bowtie2 --np 1 --cp-min 2 --rdg 28.4750311660476 --mm --score-min L,2.64955352582599,1.78754364975784 --cp-ival 2 --norc --trim3 2 --mp 8.02105962289035,2.39193168576536 --qseq -p 4 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s GTC 676s GTC 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s TGTTGAGAGGGTGACAGAGGCGTGG 676s TGTTGAGAGGGTGACAGAGGCGTGG 676s Processing line... 676s Processing line... 676s AG 676s AG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s CG 676s CG 676s Processing line... 676s AGG 676s AGG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s CA 676s CA 676s Processing line... 676s --- Summary --- 676s Read 1 reference strings 676s Checked 9 alignments, 0 edits 676s --------------- 676s PASSED 676s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 676s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 676s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 676s 33 reads; of these: 676s 32 (96.97%) were paired; of these: 676s 31 (96.88%) aligned concordantly 0 times 676s 0 (0.00%) aligned concordantly exactly 1 time 676s 1 (3.12%) aligned concordantly >1 times 676s ---- 676s 31 pairs aligned concordantly 0 times; of these: 676s 0 (0.00%) aligned discordantly 1 time 676s ---- 676s 31 pairs aligned 0 times concordantly or discordantly; of these: 676s 62 mates make up the pairs; of these: 676s 55 (88.71%) aligned 0 times 676s 3 (4.84%) aligned exactly 1 time 676s 4 (6.45%) aligned >1 times 676s 1 (3.03%) were unpaired; of these: 676s 1 (100.00%) aligned 0 times 676s 0 (0.00%) aligned exactly 1 time 676s 0 (0.00%) aligned >1 times 676s 13.85% overall alignment rate 676s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 676s Flattened IUPAC characters 676s Mutating sequence Sim.pm.2 676s Introducing 2 SNPs, 0/3 ref/read gaps, and 0 rearrangements 676s Finished SNPs 676s Finished ref gaps 676s Finished read gaps 676s Mutating sequence Sim.pm.1 676s Introducing 8 SNPs, 1/2 ref/read gaps, and 1 rearrangements 676s Finished SNPs 676s Finished ref gaps 676s Finished read gaps 676s Mutated reference genome to subject genome 676s SNPs introduced: 10 676s Reference gaps introduced: 1 676s Read gaps introduced: 5 676s Rearrangements introduced: 1 676s Created read sampler 676s Sampling 176 reads 676s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 676s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 676s parsing sequence Sim.pm.1... 676s parsing sequence Sim.pm.2... 676s Parsed 143 reference bases 676s *** Run 67 of 100 676s /usr/bin/bowtie2 -N 0 -L28 --gbar 2 --score-min L,4.76667676128798,9.44869975985004 --rfg 41.6783594915925,19.1379306305778 --rdg 9.87659735349509 --np 1 --cp-min 17 -a --cp-ival 1 -q -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq 676s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 676s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 676s Warning: skipping read '99' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 676s Warning: skipping read '100' because length (1) <= # seed mismatches (0) 676s Warning: skipping read '100' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 676s Warning: skipping read '111' because length (1) <= # seed mismatches (0) 676s Warning: skipping read '111' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 676s Warning: skipping read '129' because length (1) <= # seed mismatches (0) 676s Warning: skipping read '129' because it was < 2 characters long 676s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 676s Read 50 alignments... 676s Read 100 alignments... 676s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 676s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 676s 176 reads; of these: 676s 176 (100.00%) were unpaired; of these: 676s 127 (72.16%) aligned 0 times 676s 36 (20.45%) aligned exactly 1 time 676s 13 (7.39%) aligned >1 times 676s 27.84% overall alignment rate 676s Read 150 alignments... 676s Read 200 alignments... 676s Read 250 alignments... 676s Read 300 alignments... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s GGGTGGTGTTGAGAGGGT 676s GGGTGGTGTTGAGAGGGT 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s AGGA 676s AGGA 676s Processing line... 676s Processing line... 676s GA 676s GA 676s Processing line... 676s GA 676s GA 676s Processing line... 676s TC 676s TC 676s Processing line... 676s GA 676s GA 676s Processing line... 676s GA 676s GA 676s Processing line... 676s GA 676s GA 676s Processing line... 676s TC 676s TC 676s Processing line... 676s TC 676s TC 676s Processing line... 676s TC 676s TC 676s Processing line... 676s GA 676s GA 676s Processing line... 676s GA 676s GA 676s Processing line... 676s GA 676s GA 676s Processing line... 676s TC 676s TC 676s Processing line... 676s GA 676s GA 676s Processing line... 676s GA 676s GA 676s Processing line... 676s GA 676s GA 676s Processing line... 676s Processing line... 676s Processing line... 676s GCCCAGCTTAG 676s GCCCAGCTTAG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s CT 676s CT 676s Processing line... 676s CT 676s CT 676s Processing line... 676s AG 676s AG 676s Processing line... 676s CT 676s CT 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s CT 676s CT 676s Processing line... 676s AG 676s AG 676s Processing line... 676s CT 676s CT 676s Processing line... 676s CT 676s CT 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s Processing line... 676s TGCG 676s TGCG 676s Processing line... 676s Processing line... 676s AGCTTAGGCGGTC 676s AGCTTAGGCGGTC 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s CGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAG 676s CGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAG 676s Processing line... 676s TCGG 676s TCGG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s CCA 676s CCA 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s CCA 676s CCA 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s TGG 676s TGG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s GACTGGCG 676s GACTGGCG 676s Processing line... 676s Processing line... 676s GGGGGGGACTGGCGGGAAGACCGCGGC 676s GGGGGGGACTGGCGGGAAGACCGCGGC 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s GTGGTAGGGGGG 676s GTGGTAGGGGGG 676s Processing line... 676s CGGGTG 676s CGGGTG 676s Processing line... 676s CGGGTG 676s CGGGTG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s CGGGTGGTGTTGAGAGGGTGA 676s CGGGTGGTGTTGAGAGGGTGA 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s TCAGGA 676s TCAGGA 676s Processing line... 676s Processing line... 676s TGAGA 676s TGAGA 676s Processing line... 676s Processing line... 676s TCAGGA 676s TCAGGA 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s TTAGGCGG 676s TTAGGCGG 676s Processing line... 676s CCGGG 676s CCGGG 676s Processing line... 676s CCGGG 676s CCGGG 676s Processing line... 676s AGGGTGAC 676s AGGGTGAC 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s GT 676s GT 676s Processing line... 676s GT 676s GT 676s Processing line... 676s GT 676s GT 676s Processing line... 676s AC 676s AC 676s Processing line... 676s GT 676s GT 676s Processing line... 676s GT 676s GT 676s Processing line... 676s AC 676s AC 676s Processing line... 676s AC 676s AC 676s Processing line... 676s GT 676s GT 676s Processing line... 676s GT 676s GT 676s Processing line... 676s GT 676s GT 676s Processing line... 676s GT 676s GT 676s Processing line... 676s GT 676s GT 676s Processing line... 676s GT 676s GT 676s Processing line... 676s GT 676s GT 676s Processing line... 676s GT 676s GT 676s Processing line... 676s GT 676s GT 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s CGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAG 676s CGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s GGGGGACTG 676s GGGGGACTG 676s Processing line... 676s GGCGGTCAGGAGGGAG 676s GGCGGTCAGGAGGGAG 676s Processing line... 676s Processing line... 676s GGGGGGACT 676s GGGGGGACT 676s Processing line... 676s Processing line... 676s GGGGACTGGCG 676s GGGGACTGGCG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s CCGGGTGG 676s CCGGGTGG 676s Processing line... 676s CCGGGTGG 676s CCGGGTGG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s GTAGGGGG 676s GTAGGGGG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s TGGTGGTGGTAGGGGGGG 676s TGGTGGTGGTAGGGGGGG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s CTG 676s CTG 676s Processing line... 676s CTG 676s CTG 676s Processing line... 676s CTG 676s CTG 676s Processing line... 676s CAG 676s CAG 676s Processing line... 676s CAG 676s CAG 676s Processing line... 676s CAG 676s CAG 676s Processing line... 676s CTG 676s CTG 676s Processing line... 676s Processing line... 676s Processing line... 676s TCAGGA 676s TCAGGA 676s Processing line... 676s TAGG 676s TAGG 676s Processing line... 676s TAGG 676s TAGG 676s Processing line... 676s Processing line... 676s GGTGGTGTTGAGAGGGTG 676s GGTGGTGTTGAGAGGGTG 676s Processing line... 676s Processing line... 676s Processing line... 676s TGGTGGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCG 676s TGGTGGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCG 676s Processing line... 676s Processing line... 676s Processing line... 676s GGAGGGAGCTG 676s GGAGGGAGCTG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s TGGTGGTGGTAGGGGGGG 676s TGGTGGTGGTAGGGGGGG 676s Processing line... 676s Processing line... 676s Processing line... 676s TGGTGGTAGGGGGGG 676s TGGTGGTAGGGGGGG 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s GTAGGGGGGGACTGGCGGGAAGAC 676s GTAGGGGGGGACTGGCGGGAAGAC 676s Processing line... 676s GGAAGACCGCGGCTC 676s GGAAGACCGCGGCTC 676s Processing line... 676s Processing line... 676s AG 676s AG 676s Processing line... 676s CT 676s CT 676s Processing line... 676s CT 676s CT 676s Processing line... 676s CT 676s CT 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s CT 676s CT 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s CT 676s CT 676s Processing line... 676s CT 676s CT 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s AG 676s AG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s CC 676s CC 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s CC 676s CC 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s CC 676s CC 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s CC 676s CC 676s Processing line... 676s GG 676s GG 676s Processing line... 676s CC 676s CC 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GG 676s GG 676s Processing line... 676s GGGACTGGCGGGAAGACCGCG 676s GGGACTGGCGGGAAGACCGCG 676s Processing line... 676s Processing line... 676s GCGGGA 676s GCGGGA 676s Processing line... 676s GTAGGGGGGGACTGGCGGGAAGAC 676s GTAGGGGGGGACTGGCGGGAAGAC 676s Processing line... 676s Processing line... 676s Processing line... 676s GGCGGTCAGG 676s GGCGGTCAGG 676s Processing line... 676s GGGG 676s GGGG 676s Processing line... 676s GGGG 676s GGGG 676s Processing line... 676s GGGG 676s GGGG 676s Processing line... 676s GGGG 676s GGGG 676s Processing line... 676s GGTAGGGGGGGACTGGCGGGAA 676s GGTAGGGGGGGACTGGCGGGAA 676s Processing line... 676s Processing line... 676s Processing line... 676s --- Summary --- 676s Read 1 reference strings 676s Checked 183 alignments, 0 edits 676s --------------- 676s PASSED 676s Flattened IUPAC characters 676s Mutating sequence Sim.pm.2 676s Introducing 4 SNPs, 0/0 ref/read gaps, and 2 rearrangements 676s Finished SNPs 676s Finished ref gaps 676s Finished read gaps 676s Mutating sequence Sim.pm.1 676s Introducing 12 SNPs, 1/1 ref/read gaps, and 0 rearrangements 676s Finished SNPs 676s Finished ref gaps 676s Finished read gaps 676s Mutated reference genome to subject genome 676s SNPs introduced: 16 676s Reference gaps introduced: 1 676s Read gaps introduced: 1 676s Rearrangements introduced: 2 676s Created read sampler 676s Sampling 67 reads 676s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 676s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 676s parsing sequence Sim.pm.1... 676s parsing sequence Sim.pm.2... 676s Parsed 143 reference bases 676s *** Run 68 of 100 676s /usr/bin/bowtie2 --score-min L,2.51008634192745,2.26132690217941 --nofw --trim5 3 --cp-min 2 --cp-ival 1 --local -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 676s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '2' because it was < 2 characters long 676s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #2 of read '8' because it was < 2 characters long 676s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '10' because it was < 2 characters long 676s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '12' because it was < 2 characters long 676s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #2 of read '17' because it was < 2 characters long 676s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '21' because it was < 2 characters long 676s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '35' because it was < 2 characters long 676s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '39' because it was < 2 characters long 676s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '42' because it was < 2 characters long 676s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '54' because it was < 2 characters long 676s Read 50 alignments... 676s 67 reads; of these: 676s 61 (91.04%) were paired; of these: 676s 61 (100.00%) aligned concordantly 0 times 676s 0 (0.00%) aligned concordantly exactly 1 time 676s 0 (0.00%) aligned concordantly >1 times 676s ---- 676s 61 pairs aligned concordantly 0 times; of these: 676s 0 (0.00%) aligned discordantly 1 time 676s ---- 676s 61 pairs aligned 0 times concordantly or discordantly; of these: 676s 122 mates make up the pairs; of these: 676s 122 (100.00%) aligned 0 times 676s 0 (0.00%) aligned exactly 1 time 676s 0 (0.00%) aligned >1 times 676s 6 (8.96%) were unpaired; of these: 676s 6 (100.00%) aligned 0 times 676s 0 (0.00%) aligned exactly 1 time 676s 0 (0.00%) aligned >1 times 676s 0.00% overall alignment rate 676s Read 100 alignments... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s /usr/bin/bowtie2 --score-min L,2.51008634192745,2.26132690217941 --nofw --trim5 3 --cp-min 2 --cp-ival 1 --local -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s --- Summary --- 676s Read 1 reference strings 676s Checked 0 alignments, 0 edits 676s --------------- 676s PASSED 676s ALSO checking that bowtie2 and bowtie2-align match up 676s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '2' because it was < 2 characters long 676s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #2 of read '8' because it was < 2 characters long 676s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '10' because it was < 2 characters long 676s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '12' because it was < 2 characters long 676s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #2 of read '17' because it was < 2 characters long 676s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '21' because it was < 2 characters long 676s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '35' because it was < 2 characters long 676s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '39' because it was < 2 characters long 676s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '42' because it was < 2 characters long 676s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '54' because it was < 2 characters long 676s 67 reads; of these: 676s 61 (91.04%) were paired; of these: 676s 61 (100.00%) aligned concordantly 0 times 676s 0 (0.00%) aligned concordantly exactly 1 time 676s 0 (0.00%) aligned concordantly >1 times 676s ---- 676s 61 pairs aligned concordantly 0 times; of these: 676s 0 (0.00%) aligned discordantly 1 time 676s ---- 676s 61 pairs aligned 0 times concordantly or discordantly; of these: 676s 122 mates make up the pairs; of these: 676s 122 (100.00%) aligned 0 times 676s 0 (0.00%) aligned exactly 1 time 676s 0 (0.00%) aligned >1 times 676s 6 (8.96%) were unpaired; of these: 676s 6 (100.00%) aligned 0 times 676s 0 (0.00%) aligned exactly 1 time 676s 0 (0.00%) aligned >1 times 676s 0.00% overall alignment rate 676s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 676s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 676s /usr/bin/bowtie2 --score-min L,2.51008634192745,2.26132690217941 --nofw --trim5 3 --cp-min 2 --cp-ival 1 --local -r -p 3 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 676s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '2' because it was < 2 characters long 676s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #2 of read '8' because it was < 2 characters long 676s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '10' because it was < 2 characters long 676s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '12' because it was < 2 characters long 676s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #2 of read '17' because it was < 2 characters long 676s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '21' because it was < 2 characters long 676s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '35' because it was < 2 characters long 676s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '39' because it was < 2 characters long 676s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '42' because it was < 2 characters long 676s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '54' because it was < 2 characters long 676s 67 reads; of these: 676s 61 (91.04%) were paired; of these: 676s 61 (100.00%) aligned concordantly 0 times 676s 0 (0.00%) aligned concordantly exactly 1 time 676s 0 (0.00%) aligned concordantly >1 times 676s ---- 676s 61 pairs aligned concordantly 0 times; of these: 676s 0 (0.00%) aligned discordantly 1 time 676s ---- 676s 61 pairs aligned 0 times concordantly or discordantly; of these: 676s 122 mates make up the pairs; of these: 676s 122 (100.00%) aligned 0 times 676s 0 (0.00%) aligned exactly 1 time 676s 0 (0.00%) aligned >1 times 676s 6 (8.96%) were unpaired; of these: 676s 6 (100.00%) aligned 0 times 676s 0 (0.00%) aligned exactly 1 time 676s 0 (0.00%) aligned >1 times 676s 0.00% overall alignment rate 676s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 676s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 676s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 676s Flattened IUPAC characters 676s Mutating sequence Sim.pm.2 676s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 676s Finished SNPs 676s Finished ref gaps 676s Finished read gaps 676s Mutating sequence Sim.pm.1 676s Introducing 2 SNPs, 2/1 ref/read gaps, and 2 rearrangements 676s Finished SNPs 676s Finished ref gaps 676s Finished read gaps 676s Mutated reference genome to subject genome 676s SNPs introduced: 4 676s Reference gaps introduced: 2 676s Read gaps introduced: 2 676s Rearrangements introduced: 3 676s Created read sampler 676s Sampling 90 reads 676s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 676s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 676s parsing sequence Sim.pm.1... 676s parsing sequence Sim.pm.2... 676s Parsed 143 reference bases 676s *** Run 69 of 100 676s /usr/bin/bowtie2 --mp 1.76850105045484,1.42808618321425 --trim3 4 --cp-ival 1 --local --norc --trim5 1 --mm --rdg 18.0809419620224,17.4532130130209 -D 48 --score-min L,9.66967569986472,5.88029728216365 --np 3 --cp-min 10 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 676s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '3' because it was < 2 characters long 676s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '6' because it was < 2 characters long 676s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '12' because it was < 2 characters long 676s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '23' because it was < 2 characters long 676s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '25' because it was < 2 characters long 676s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '31' because it was < 2 characters long 676s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '32' because it was < 2 characters long 676s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '42' because it was < 2 characters long 676s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '56' because it was < 2 characters long 676s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '62' because it was < 2 characters long 676s Read 50 alignments... 676s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '69' because it was < 2 characters long 676s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '75' because it was < 2 characters long 676s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '76' because it was < 2 characters long 676s Read 100 alignments... 676s 90 reads; of these: 676s 81 (90.00%) were paired; of these: 676s 81 (100.00%) aligned concordantly 0 times 676s 0 (0.00%) aligned concordantly exactly 1 time 676s 0 (0.00%) aligned concordantly >1 times 676s ---- 676s 81 pairs aligned concordantly 0 times; of these: 676s 0 (0.00%) aligned discordantly 1 time 676s ---- 676s 81 pairs aligned 0 times concordantly or discordantly; of these: 676s 162 mates make up the pairs; of these: 676s 162 (100.00%) aligned 0 times 676s 0 (0.00%) aligned exactly 1 time 676s 0 (0.00%) aligned >1 times 676s 9 (10.00%) were unpaired; of these: 676s 9 (100.00%) aligned 0 times 676s 0 (0.00%) aligned exactly 1 time 676s 0 (0.00%) aligned >1 times 676s 0.00% overall alignment rate 676s Read 150 alignments... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s /usr/bin/bowtie2 --mp 1.76850105045484,1.42808618321425 --trim3 4 --cp-ival 1 --local --norc --trim5 1 --mm --rdg 18.0809419620224,17.4532130130209 -D 48 --score-min L,9.66967569986472,5.88029728216365 --np 3 --cp-min 10 -r -p 4 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s Processing line... 676s --- Summary --- 676s Read 1 reference strings 676s Checked 0 alignments, 0 edits 676s --------------- 676s PASSED 676s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 676s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '3' because it was < 2 characters long 676s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '6' because it was < 2 characters long 676s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '12' because it was < 2 characters long 676s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '23' because it was < 2 characters long 676s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '25' because it was < 2 characters long 676s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '31' because it was < 2 characters long 676s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '32' because it was < 2 characters long 676s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '42' because it was < 2 characters long 676s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '56' because it was < 2 characters long 676s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '62' because it was < 2 characters long 676s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '69' because it was < 2 characters long 676s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 676s Warning: skipping read '75' because it was < 2 characters long 676s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 676s Warning: skipping mate #1 of read '76' because it was < 2 characters long 676s 90 reads; of these: 676s 81 (90.00%) were paired; of these: 676s 81 (100.00%) aligned concordantly 0 times 676s 0 (0.00%) aligned concordantly exactly 1 time 676s 0 (0.00%) aligned concordantly >1 times 676s ---- 676s 81 pairs aligned concordantly 0 times; of these: 676s 0 (0.00%) aligned discordantly 1 time 676s ---- 676s 81 pairs aligned 0 times concordantly or discordantly; of these: 676s 162 mates make up the pairs; of these: 676s 162 (100.00%) aligned 0 times 676s 0 (0.00%) aligned exactly 1 time 676s 0 (0.00%) aligned >1 times 676s 9 (10.00%) were unpaired; of these: 676s 9 (100.00%) aligned 0 times 676s 0 (0.00%) aligned exactly 1 time 676s 0 (0.00%) aligned >1 times 676s 0.00sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 676s % overall alignment rate 676s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 676s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 676s /usr/bin/bowtie2 --mp 1.76850105045484,1.42808618321425 --trim3 4 --cp-ival 1 --local --norc --trim5 1 --mm --rdg 18.0809419620224,17.4532130130209 -D 48 --score-min L,9.66967569986472,5.88029728216365 --np 3 --cp-min 10 -r -p 2 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 676s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 677s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 677s Warning: skipping mate #1 of read '3' because it was < 2 characters long 677s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 677s Warning: skipping read '6' because it was < 2 characters long 677s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 677s Warning: skipping mate #1 of read '12' because it was < 2 characters long 677s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 677s Warning: skipping mate #1 of read '23' because it was < 2 characters long 677s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 677s Warning: skipping mate #1 of read '25' because it was < 2 characters long 677s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 677s Warning: skipping mate #1 of read '31' because it was < 2 characters long 677s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 677s Warning: skipping mate #1 of read '32' because it was < 2 characters long 677s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 677s Warning: skipping mate #1 of read '42' because it was < 2 characters long 677s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (0) 677s Warning: skipping mate #1 of read '56' because it was < 2 characters long 677s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 677s Warning: skipping mate #1 of read '62' because it was < 2 characters long 677s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 677s Warning: skipping mate #1 of read '69' because it was < 2 characters long 677s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 677s Warning: skipping read '75' because it was < 2 characters long 677s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 677s Warning: skipping mate #1 of read '76' because it was < 2 characters long 677s 90 reads; of these: 677s 81 (90.00%) were paired; of these: 677s 81 (100.00%) aligned concordantly 0 times 677s 0 (0.00%) aligned concordantly exactly 1 time 677s 0 (0.00%) aligned concordantly >1 times 677s ---- 677s 81 pairs aligned concordantly 0 times; of these: 677s 0 (0.00%) aligned discordantly 1 time 677s ---- 677s 81 pairs aligned 0 times concordantly or discordantly; of these: 677s 162 mates make up the pairs; of these: 677s 162 (100.00%) aligned 0 times 677s 0 (0.00%) aligned exactly 1 time 677s 0 (0.00%) aligned >1 times 677s 9 (10.00%) were unpaired; of these: 677s 9 (100.00%) aligned 0 times 677s 0 (0.00%) aligned exactly 1 time 677s 0 (0.00%) aligned >1 times 677s 0.00% overall alignment rate 677s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 677s Flattened IUPAC characters 677s Mutating sequence Sim.pm.1 677s Introducing 14 SNPs, 1/0 ref/read gaps, and 0 rearrangements 677s Finished SNPs 677s Finished ref gaps 677s Finished read gaps 677s Mutating sequence Sim.pm.2 677s Introducing 3 SNPs, 1/1 ref/read gaps, and 0 rearrangements 677s Finished SNPs 677s Finished ref gaps 677s Finished read gaps 677s Mutated reference genome to subject genome 677s SNPs introduced: 17 677s Reference gaps introduced: 2 677s Read gaps introduced: 1 677s Rearrangements introduced: 0 677s Created read sampler 677s Sampling 42 reads 677s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 677s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 677s parsing sequence Sim.pm.1... 677s parsing sequence Sim.pm.2... 677s Parsed 143 reference bases 677s *** Run 70 of 100 677s /usr/bin/bowtie2 --ma 19.1823879361632 --score-min L,7.29618248677604,9.4239998618327 --mm --cp-min 2 --np 4 --mp 6.31955166867091,1.06719166026976 --rfg 1.70124079641209 --n-ceil 0.971314051682919,1.2601395419854 --trim5 4 --cp-ival 1 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 677s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 677s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 677s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 677s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 677s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 677s 42 reads; of these: 677s 36 (85.71%) were paired; of these: 677s 36 (100.00%) aligned concordantly 0 times 677s 0 (0.00%) aligned concordantly exactly 1 time 677s 0 (0.00%) aligned concordantly >1 times 677s ---- 677s 36 pairs aligned concordantly 0 times; of these: 677s 1 (2.78%) aligned discordantly 1 time 677s ---- 677s 35 pairs aligned 0 times concordantly or discordantly; of these: 677s 70 mates make up the pairs; of these: 677s 64 (91.43%) aligned 0 times 677s 3 (4.29%) aligned exactly 1 time 677s 3 (4.29%) aligned >1 times 677s 6 (14.29%) were unpaired; of these: 677s 6 (100.00%) aligned 0 times 677s 0 (0.00%) aligned exactly 1 time 677s 0 (0.00%) aligned >1 times 677s 10.26% overall alignment rate 677s Read 50 alignments... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s GGCTCGGTCTGCGCCCAGC 677s GGCTCGGTCTGCGCCCAGC 677s Processing line... 677s TGCGCCCA 677s TGCGCCCA 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s GGTAGGGGGGGACT 677s GGTAGGGGGGGACT 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s TAGGGGGGGACTGGCGGG 677s TAGGGGGGGACTGGCGGG 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s CTGG 677s CTGG 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s TGG 677s TGG 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s GCGT 677s GCGT 677s Processing line... 677s CAGGAGGGAGCTGG 677s CAGGAGGGAGCTGG 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s --- Summary --- 677s Read 1 reference strings 677s Checked 8 alignments, 0 edits 677s --------------- 677s PASSED 677s Flattened IUPAC characters 677s Mutating sequence Sim.pm.1 677s Introducing 17 SNPs, 3/1 ref/read gaps, and 2 rearrangements 677s Finished SNPs 677s Finished ref gaps 677s Finished read gaps 677s Mutating sequence Sim.pm.2 677s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 677s Finished SNPs 677s Finished ref gaps 677s Finished read gaps 677s Mutated reference genome to subject genome 677s SNPs introduced: 24 677s Reference gaps introduced: 3 677s Read gaps introduced: 2 677s Rearrangements introduced: 2 677s Created read sampler 677s Sampling 41 reads 677s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 677s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 677s parsing sequence Sim.pm.1... 677s parsing sequence Sim.pm.2... 677s Parsed 143 reference bases 677s *** Run 71 of 100 677s /usr/bin/bowtie2 --cp-ival 2 -M 2 --cp-min 3 --rdg 3.47679874092708,5.0425097023199 --mm --score-min L,5.96171734516787,3.29179214257856 --trim3 6 --mp 7.06346327364183,5.53334332319637 -N 1 -L30 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 677s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 677s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 677s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '1' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 677s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '2' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 677s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '3' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 677s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '6' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 677s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '7' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 677s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '9' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 677s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '11' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 677s Warning: skipping read '15' because length (1) <= # seed mismatches (1) 677s Warning: skipping read '15' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 677s Warning: skipping read '20' because length (1) <= # seed mismatches (1) 677s Warning: skipping read '20' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 677s Warning: skipping read '23' because length (1) <= # seed mismatches (1) 677s Warning: skipping read '23' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 677s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '28' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 677s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '32' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 677s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '33' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 677s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '34' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 677s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '41' because it was < 2 characters long 677s 41 reads; of these: 677s 41 (100.00%) were unpaired; of these: 677s 33 (80.49%) aligned 0 times 677s 4 (9.76%) aligned exactly 1 time 677s 4 (9.76%) aligned >1 times 677s 19.51% overall alignment rate 677s Processing line... 677s Processing line... 677s Processing line... 677s /usr/bin/bowtie2 --cp-ival 2 -M 2 --cp-min 3 --rdg 3.47679874092708,5.0425097023199 --mm --score-min L,5.96171734516787,3.29179214257856 --trim3 6 --mp 7.06346327364183,5.53334332319637 -N 1 -L30 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s GT 677s GT 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s TGCG 677s TGCG 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s GTA 677s GTA 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s TCCG 677s TCCG 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s GGCTCGGT 677s GGCTCGGT 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s AGGCGTG 677s AGGCGTG 677s Processing line... 677s Processing line... 677s AGAGGG 677s AGAGGG 677s Processing line... 677s CT 677s CT 677s Processing line... 677s Processing line... 677s --- Summary --- 677s Read 1 reference strings 677s Checked 8 alignments, 0 edits 677s --------------- 677s PASSED 677s ALSO checking that bowtie2 and bowtie2-align match up 677s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 677s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 677s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '1' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 677s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '2' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 677s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '3' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 677s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '6' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 677s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '7' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 677s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '9' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 677s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '11' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 677s Warning: skipping read '15' because length (1) <= # seed mismatches (1) 677s Warning: skipping read '15' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 677s Warning: skipping read '20' because length (1) <= # seed mismatches (1) 677s Warning: skipping read '20' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 677s Warning: skipping read '23' because length (1) <= # seed mismatches (1) 677s Warning: skipping read '23' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 677s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '28' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 677s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '32' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 677s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '33' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 677s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '34' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 677s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '41' because it was < 2 characters long 677s 41 reads; of these: 677s 41 (100.00%) were unpaired; of these: 677s 33 (80.49%) aligned 0 times 677s 4 (9.76%) aligned exactly 1 time 677s 4 (9.76%) aligned >1 times 677s 19.51% overall alignment rate 677s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 677s /usr/bin/bowtie2 --cp-ival 2 -M 2 --cp-min 3 --rdg 3.47679874092708,5.0425097023199 --mm --score-min L,5.96171734516787,3.29179214257856 --trim3 6 --mp 7.06346327364183,5.53334332319637 -N 1 -L30 -f -p 3 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 677s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 677s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 677s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 677s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '1' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 677s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '2' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 677s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '3' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 677s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '6' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 677s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '7' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 677s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '9' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 677s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '11' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 677s Warning: skipping read '15' because length (1) <= # seed mismatches (1) 677s Warning: skipping read '15' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 677s Warning: skipping read '20' because length (1) <= # seed mismatches (1) 677s Warning: skipping read '20' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 677s Warning: skipping read '23' because length (1) <= # seed mismatches (1) 677s Warning: skipping read '23' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 677s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '28' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 677s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '32' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 677s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '33' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 677s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '34' because it was < 2 characters long 677s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 677s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 677s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 677s Warning: skipping read '41' because it was < 2 characters long 677s 41 reads; of these: 677s 41 (100.00%) were unpaired; of these: 677s 33 (80.49%) aligned 0 times 677s 4 (9.76%) aligned exactly 1 time 677s 4 (9.76%) aligned >1 times 677s 19.51% overall alignment rate 677s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 677s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 677s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 677s Flattened IUPAC characters 677s Mutating sequence Sim.pm.2 677s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 677s Finished SNPs 677s Finished ref gaps 677s Finished read gaps 677s Mutating sequence Sim.pm.1 677s Introducing 13 SNPs, 2/1 ref/read gaps, and 2 rearrangements 677s Finished SNPs 677s Finished ref gaps 677s Finished read gaps 677s Mutated reference genome to subject genome 677s SNPs introduced: 16 677s Reference gaps introduced: 3 677s Read gaps introduced: 1 677s Rearrangements introduced: 2 677s Created read sampler 677s Sampling 33 reads 677s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 677s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 677s *** Run 72 of 100 677s /usr/bin/bowtie2 --cp-ival 2 --local --rfg 9.7382471048045,13.1713351698422 --mp 8.52164271675965,4.92690918072466 -i L --trim3 6 --nofw --cp-min 4 --rdg 21.9377783670608,18.3086399758395 -R 3 --gbar 2 --score-min L,3.53800013090019,7.95956826888179 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 677s parsing sequence Sim.pm.1... 677s parsing sequence Sim.pm.2... 677s Parsed 143 reference bases 677s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 677s Warning: skipping read '22' because it was < 2 characters long 677s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 677s Warning: skipping read '25' because it was < 2 characters long 677s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 677s Warning: skipping read '33' because it was < 2 characters long 677s 33 reads; of these: 677s 33 (100.00%) were unpaired; of these: 677s 33 (100.00%) aligned 0 times 677s 0 (0.00%) aligned exactly 1 time 677s 0 (0.00%) aligned >1 times 677s 0.00% overall alignment rate 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s --- Summary --- 677s Read 1 reference strings 677s Checked 0 alignments, 0 edits 677s --------------- 677s PASSED 677s Flattened IUPAC characters 677s Mutating sequence Sim.pm.2 677s Introducing 7 SNPs, 0/2 ref/read gaps, and 0 rearrangements 677s Finished SNPs 677s Finished ref gaps 677s Finished read gaps 677s Mutating sequence Sim.pm.1 677s Introducing 12 SNPs, 2/1 ref/read gaps, and 1 rearrangements 677s Finished SNPs 677s Finished ref gaps 677s Finished read gaps 677s Mutated reference genome to subject genome 677s SNPs introduced: 19 677s Reference gaps introduced: 2 677s Read gaps introduced: 3 677s Rearrangements introduced: 1 677s Created read sampler 677s Sampling 108 reads 677s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 677s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 677s parsing sequence Sim.pm.1... 677s *** Run 73 of 100 677s /usr/bin/bowtie2 --rfg 28.0954320715329,1.39193812306725 --mm --score-min L,4.74469804824299,2.29966219583121 --mp 5.72817549849624,1.88008033801188 --local --cp-ival 1 --np 2 --cp-min 2 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 677s parsing sequence Sim.pm.2... 677s Parsed 143 reference bases 677s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 677s Warning: skipping read '47' because it was < 2 characters long 677s Warning: skipping read '85' because length (1) <= # seed mismatches (0) 677s Warning: skipping read '85' because it was < 2 characters long 677s 108 reads; of these: 677s 108 (100.00%) were unpaired; of these: 677s 108 (100.00%) aligned 0 times 677s 0 (0.00%) aligned exactly 1 time 677s 0 (0.00%) aligned >1 times 677s 0.00% overall alignment rate 677s Read 50 alignments... 677s Read 100 alignments... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s /usr/bin/bowtie2 --rfg 28.0954320715329,1.39193812306725 --mm --score-min L,4.74469804824299,2.29966219583121 --mp 5.72817549849624,1.88008033801188 --local --cp-ival 1 --np 2 --cp-min 2 -f -p 4 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s Processing line... 677s --- Summary --- 677s Read 1 reference strings 677s Checked 0 alignments, 0 edits 677s --------------- 677s PASSED 677s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 677s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 677s Warning: skipping read '47' because it was < 2 characters long 677s Warning: skipping read '85' because length (1) <= # seed mismatches (0) 677s Warning: skipping read '85' because it was < 2 characters long 678s 108 reads; of these: 678s 108 (100.00%) were unpaired; of these: 678s 108 (100.00%) aligned 0 times 678s 0 (0.00%) aligned exactly 1 time 678s 0 (0.00%) aligned >1 times 678s 0.00% overall alignment rate 678s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 678s Flattened IUPAC characters 678s Mutating sequence Sim.pm.1 678s Introducing 17 SNPs, 0/0 ref/read gaps, and 1 rearrangements 678s Finished SNPs 678s Finished ref gaps 678s Finished read gaps 678s Mutating sequence Sim.pm.2 678s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 678s Finished SNPs 678s Finished ref gaps 678s Finished read gaps 678s Mutated reference genome to subject genome 678s SNPs introduced: 20 678s Reference gaps introduced: 0 678s Read gaps introduced: 0 678s Rearrangements introduced: 1 678s Created read sampler 678s Sampling 67 reads 678s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 678s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 678s parsing sequence Sim.pm.1... 678s *** Run 74 of 100 678s /usr/bin/bowtie2 --rdg 12.5185933234545 --score-min L,7.89376376754135,2.75845802643752 --gbar 2 -i L --local --cp-ival 1 --cp-min 3 --np 5 --trim5 2 -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta 678s parsing sequence Sim.pm.2... 678s Parsed 143 reference bases 678s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '1' because it was < 2 characters long 678s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #2 of read '8' because it was < 2 characters long 678s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #2 of read '20' because it was < 2 characters long 678s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '24' because it was < 2 characters long 678s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '29' because it was < 2 characters long 678s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #2 of read '39' because it was < 2 characters long 678s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '48' because it was < 2 characters long 678s Read 50 alignments... 678s 67 reads; of these: 678s 66 (98.51%) were paired; of these: 678s 66 (100.00%) aligned concordantly 0 times 678s 0 (0.00%) aligned concordantly exactly 1 time 678s 0 (0.00%) aligned concordantly >1 times 678s ---- 678s 66 pairs aligned concordantly 0 times; of these: 678s 0 (0.00%) aligned discordantly 1 time 678s ---- 678s 66 pairs aligned 0 times concordantly or discordantly; of these: 678s 132 mates make up the pairs; of these: 678s 132 (100.00%) aligned 0 times 678s 0 (0.00%) aligned exactly 1 time 678s 0 (0.00%) aligned >1 times 678s 1 (1.49%) were unpaired; of these: 678s 1 (100.00%) aligned 0 times 678s 0 (0.00%) aligned exactly 1 time 678s 0 (0.00%) aligned >1 times 678s 0.00% overall alignment rate 678s Read 100 alignments... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s 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line... 678s Processing line... 678s --- Summary --- 678s Read 1 reference strings 678s Checked 0 alignments, 0 edits 678s --------------- 678s PASSED 678s Flattened IUPAC characters 678s Mutating sequence Sim.pm.1 678s Introducing 1 SNPs, 1/3 ref/read gaps, and 2 rearrangements 678s Finished SNPs 678s Finished ref gaps 678s Finished read gaps 678s Mutating sequence Sim.pm.2 678s Introducing 4 SNPs, 3/1 ref/read gaps, and 1 rearrangements 678s Finished SNPs 678s Finished ref gaps 678s Finished read gaps 678s Mutated reference genome to subject genome 678s SNPs introduced: 5 678s Reference gaps introduced: 4 678s Read gaps introduced: 4 678s Rearrangements introduced: 3 678s Created read sampler 678s Sampling 147 reads 678s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 678s *** Run 75 of 100 678s /usr/bin/bowtie2 --np 1 --cp-min 16 -a --n-ceil 1.00789805765792,0.155756272719839 --cp-ival 1 --score-min L,2.26217277873526,9.86849367563704 --mp 6.1914602617147,3.71891534566311 -R 1 -N 0 -L22 --rfg 43.5392627640801 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 678s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 678s parsing sequence Sim.pm.1... 678s parsing sequence Sim.pm.2... 678s Parsed 143 reference bases 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 678s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '18' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 678s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '24' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 678s Read 50 alignments... 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 678s Read 100 alignments... 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 678s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '62' because it was < 2 characters long 678s Warning: skipping mate #2 of read '62' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 678s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #2 of read '66' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 678s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '96' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 678s Read 150 alignments... 678s Read 200 alignments... 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 678s Warning: skipping mate #2 of read '124' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #2 of read '124' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 678s Read 250 alignments... 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 678s Read 300 alignments... 678s Read 350 alignments... 678s 147 reads; of these: 678s 147 (100.00%) were paired; of these: 678s 145 (98.64%) aligned concordantly 0 times 678s 0 (0.00%) aligned concordantly exactly 1 time 678s 2 (1.36%) aligned concordantly >1 times 678s ---- 678s 145 pairs aligned concordantly 0 times; of these: 678s 0 (0.00%) aligned discordantly 1 time 678s ---- 678s 145 pairs aligned 0 times concordantly or discordantly; of these: 678s 290 mates make up the pairs; of these: 678s 225 (77.59%) aligned 0 times 678s 42 (14.48%) aligned exactly 1 time 678s 23 (7.93%) aligned >1 times 678s 23.47% overall alignment rate 678s Read 400 alignments... 678s Read 450 alignments... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s TCGGTCTGC 678s TCGGTCTGC 678s Processing line... 678s Processing line... 678s TCGGTCTGCGCCCAGCTTAGGCGGTCAGG 678s TCGGTCTGCGCCCAGCTTAGGCGGTCAGG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s CCG 678s CCG 678s Processing line... 678s CCG 678s CCG 678s Processing line... 678s CGG 678s CGG 678s Processing line... 678s CGG 678s CGG 678s Processing line... 678s CGG 678s CGG 678s Processing line... 678s CGG 678s CGG 678s Processing line... 678s CCG 678s CCG 678s Processing line... 678s CGG 678s CGG 678s Processing line... 678s CGG 678s CGG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s AC 678s AC 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s AC 678s AC 678s Processing line... 678s AC 678s AC 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s CCGGGTGGTGTT 678s CCGGGTGGTGTT 678s Processing line... 678s CCGGGTGGTGTT 678s CCGGGTGGTGTT 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GA 678s GA 678s Processing line... 678s TC 678s TC 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s TC 678s TC 678s Processing line... 678s TC 678s TC 678s Processing line... 678s TC 678s TC 678s Processing line... 678s TC 678s TC 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s Processing line... 678s GTG 678s GTG 678s Processing line... 678s GTG 678s GTG 678s Processing line... 678s GTG 678s GTG 678s Processing line... 678s GTG 678s GTG 678s Processing line... 678s GTG 678s GTG 678s Processing line... 678s GTG 678s GTG 678s Processing line... 678s GTG 678s GTG 678s Processing line... 678s GTG 678s GTG 678s Processing line... 678s GTG 678s GTG 678s Processing line... 678s Processing line... 678s GGGTGGTGTTGAGAGGGTGACAGA 678s GGGTGGTGTTGAGAGGGTGACAGA 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GGGACTGGCGGGAA 678s GGGACTGGCGGGAA 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGG 678s GCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GTGTTGAGA 678s GTGTTGAGA 678s Processing line... 678s Processing line... 678s GCGCCCAGC 678s GCGCCCAGC 678s Processing line... 678s Processing line... 678s TGGTAGGGGGGGACTGGCG 678s TGGTAGGGGGGGACTGGCG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s AGAGG 678s AGAGG 678s Processing line... 678s AGAGG 678s AGAGG 678s Processing line... 678s AGAGG 678s AGAGG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s CTG 678s CTG 678s Processing line... 678s CAG 678s CAG 678s Processing line... 678s CAG 678s CAG 678s Processing line... 678s CTG 678s CTG 678s Processing line... 678s CAG 678s CAG 678s Processing line... 678s CTG 678s CTG 678s Processing line... 678s CTG 678s CTG 678s Processing line... 678s Processing line... 678s TGGTGTTGAGAGGGTGACAGAGGCG 678s TGGTGTTGAGAGGGTGACAGAGGCG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s TCCGGGTGGTGTTGAGAGG 678s TCCGGGTGGTGTTGAGAGG 678s Processing line... 678s Processing line... 678s CAGCTTAG 678s CAGCTTAG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GTGGTAGGG 678s GTGGTAGGG 678s Processing line... 678s Processing line... 678s GTAGGG 678s GTAGGG 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GTAGGG 678s GTAGGG 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GTAGGG 678s GTAGGG 678s Processing line... 678s GT 678s GT 678s Processing line... 678s TCCGG 678s TCCGG 678s Processing line... 678s TCCGG 678s TCCGG 678s Processing line... 678s CGTG 678s CGTG 678s Processing line... 678s CGTG 678s CGTG 678s Processing line... 678s GAA 678s GAA 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s AC 678s AC 678s Processing line... 678s AC 678s AC 678s Processing line... 678s AC 678s AC 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s GT 678s GT 678s Processing line... 678s Processing line... 678s TCTGCGCCCAGC 678s TCTGCGCCCAGC 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s CTGGTGGTGGTAGGGGGGGACTGGCGGGAA 678s CTGGTGGTGGTAGGGGGGGACTGGCGGGAA 678s Processing line... 678s Processing line... 678s AGG 678s AGG 678s Processing line... 678s AGG 678s AGG 678s Processing line... 678s AGG 678s AGG 678s Processing line... 678s AGG 678s AGG 678s Processing line... 678s AGG 678s AGG 678s Processing line... 678s AGG 678s AGG 678s Processing line... 678s AGG 678s AGG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s TCGGTCTGCGCCCAGCTTAGGCGGT 678s TCGGTCTGCGCCCAGCTTAGGCGGT 678s Processing line... 678s Processing line... 678s ACTGGCGGGAAGA 678s ACTGGCGGGAAGA 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s GC 678s GC 678s Processing line... 678s Processing line... 678s TCCGGGTGGTGTTGAGAGGGTGACAGAGGCG 678s TCCGGGTGGTGTTGAGAGGGTGACAGAGGCG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s TCCGGGTGGTGTTGAGAGGGTGACAGAGG 678s TCCGGGTGGTGTTGAGAGGGTGACAGAGG 678s Processing line... 678s Processing line... 678s GA 678s GA 678s Processing line... 678s TC 678s TC 678s Processing line... 678s TC 678s TC 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s TC 678s TC 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s TC 678s TC 678s Processing line... 678s GA 678s GA 678s Processing line... 678s TC 678s TC 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s GA 678s GA 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s AGGGGGGGACTGGC 678s AGGGGGGGACTGGC 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s AGCTTAGGCGGTCAGGAGGG 678s AGCTTAGGCGGTCAGGAGGG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GCT 678s GCT 678s Processing line... 678s AGC 678s AGC 678s Processing line... 678s GCT 678s GCT 678s Processing line... 678s AGC 678s AGC 678s Processing line... 678s GCT 678s GCT 678s Processing line... 678s TAGGGGGG 678s TAGGGGGG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s ACAGAGGCGT 678s ACAGAGGCGT 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s AGGGTGACAGAGGCGTG 678s AGGGTGACAGAGGCGTG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s CAGGAGGG 678s CAGGAGGG 678s Processing line... 678s Processing line... 678s TGGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCG 678s TGGTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCG 678s Processing line... 678s Processing line... 678s GCGGCTCGGTCTG 678s GCGGCTCGGTCTG 678s Processing line... 678s Processing line... 678s CGTGG 678s CGTGG 678s Processing line... 678s CGTGG 678s CGTGG 678s Processing line... 678s Processing line... 678s GAGAGGGTGACAGAGGC 678s GAGAGGGTGACAGAGGC 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s TGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGC 678s TGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGC 678s Processing line... 678s Processing line... 678s GAGAGGGTGACAG 678s GAGAGGGTGACAG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s TGCGCCCAG 678s TGCGCCCAG 678s Processing line... 678s Processing line... 678s ACCGCGGCTCGGTCTGCGCCCAGCTTA 678s ACCGCGGCTCGGTCTGCGCCCAGCTTA 678s Processing line... 678s Processing line... 678s AGAGGGTGACA 678s AGAGGGTGACA 678s Processing line... 678s Processing line... 678s TCTGCGCCCAGC 678s TCTGCGCCCAGC 678s Processing line... 678s CCGCGG 678s CCGCGG 678s Processing line... 678s CCGCGG 678s CCGCGG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GGGGGGAC 678s GGGGGGAC 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s TTGA 678s TTGA 678s Processing line... 678s TTGA 678s TTGA 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s TG 678s TG 678s Processing line... 678s TG 678s TG 678s Processing line... 678s TG 678s TG 678s Processing line... 678s TG 678s TG 678s Processing line... 678s TG 678s TG 678s Processing line... 678s TG 678s TG 678s Processing line... 678s TG 678s TG 678s Processing line... 678s TG 678s TG 678s Processing line... 678s TG 678s TG 678s Processing line... 678s TG 678s TG 678s Processing line... 678s TG 678s TG 678s Processing line... 678s TG 678s TG 678s Processing line... 678s TG 678s TG 678s Processing line... 678s CA 678s CA 678s Processing line... 678s TG 678s TG 678s Processing line... 678s CA 678s CA 678s Processing line... 678s CA 678s CA 678s Processing line... 678s TG 678s TG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s TCGGTCTGCGCCCAGC 678s TCGGTCTGCGCCCAGC 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GCGCCCA 678s GCGCCCA 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GAG 678s GAG 678s Processing line... 678s GAG 678s GAG 678s Processing line... 678s GAG 678s GAG 678s Processing line... 678s GAG 678s GAG 678s Processing line... 678s GAG 678s GAG 678s Processing line... 678s CTC 678s CTC 678s Processing line... 678s GAG 678s GAG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GAGAGGGTGACAGAGGCGT 678s GAGAGGGTGACAGAGGCGT 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GGTGGTGTTGAGAGGGTGACAGAGG 678s GGTGGTGTTGAGAGGGTGACAGAGG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GACTGGCGG 678s GACTGGCGG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s TGG 678s TGG 678s Processing line... 678s TGG 678s TGG 678s Processing line... 678s CCA 678s CCA 678s Processing line... 678s TGG 678s TGG 678s Processing line... 678s TGG 678s TGG 678s Processing line... 678s TGG 678s TGG 678s Processing line... 678s TGG 678s TGG 678s Processing line... 678s TGG 678s TGG 678s Processing line... 678s TGG 678s TGG 678s Processing line... 678s TGG 678s TGG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s TGGTGTTG 678s TGGTGTTG 678s Processing line... 678s TGGTGTTG 678s TGGTGTTG 678s Processing line... 678s Processing line... 678s GGTGGTGGTAGGGGGG 678s GGTGGTGGTAGGGGGG 678s Processing line... 678s CC 678s CC 678s Processing line... 678s GGTGGTGGTAGGGGGG 678s GGTGGTGGTAGGGGGG 678s Processing line... 678s CC 678s CC 678s Processing line... 678s GGTGGTGGTAGGGGGG 678s GGTGGTGGTAGGGGGG 678s Processing line... 678s CC 678s CC 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s GGGGGACTGGCGGGAAGACCGC 678s GGGGGACTGGCGGGAAGACCGC 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s AGGG 678s AGGG 678s Processing line... 678s AGGG 678s AGGG 678s Processing line... 678s AGGG 678s AGGG 678s Processing line... 678s Processing line... 678s GGG 678s GGG 678s Processing line... 678s GGG 678s GGG 678s Processing line... 678s CCC 678s CCC 678s Processing line... 678s GGG 678s GGG 678s Processing line... 678s GGG 678s GGG 678s Processing line... 678s GGG 678s GGG 678s Processing line... 678s GGG 678s GGG 678s Processing line... 678s GGG 678s GGG 678s Processing line... 678s GGG 678s GGG 678s Processing line... 678s GGG 678s GGG 678s Processing line... 678s GGG 678s GGG 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s Processing line... 678s CTGCGCCCAGCTTAG 678s CTGCGCCCAGCTTAG 678s Processing line... 678s Processing line... 678s Processing line... 678s --- Summary --- 678s Read 1 reference strings 678s Checked 243 alignments, 0 edits 678s /usr/bin/bowtie2 --np 1 --cp-min 16 -a --n-ceil 1.00789805765792,0.155756272719839 --cp-ival 1 --score-min L,2.26217277873526,9.86849367563704 --mp 6.1914602617147,3.71891534566311 -R 1 -N 0 -L22 --rfg 43.5392627640801 -q -p 4 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 678s --------------- 678s PASSED 678s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 678s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '18' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 678s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '24' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 678s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '62' because it was < 2 characters long 678s Warning: skipping mate #2 of read '62' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 678s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #2 of read '66' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 678s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '96' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 678s Warning: skipping mate #2 of read '124' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #2 of read '124' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 678s 147 reads; of these: 678s 147 (100.00%) were paired; of these: 678s 145 (98.64%) aligned concordantly 0 times 678s 0 (0.00%) aligned concordantly exactly 1 time 678s 2 (1.36%) aligned concordantly >1 times 678s ---- 678s 145 pairs aligned concordantly 0 times; of these: 678s 0 (0.00%) aligned discordantly 1 time 678s ---- 678s 145 pairs aligned 0 times concordantly or discordantly; of these: 678s 290 mates make up the pairs; of these: 678s 225 (77.59%) aligned 0 times 678s 42 (14.48%) aligned exactly 1 time 678s 23 (7.93%) aligned >1 times 678s 23.47% overall alignment rate 678s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 678s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 678s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 678s /usr/bin/bowtie2 --np 1 --cp-min 16 -a --n-ceil 1.00789805765792,0.155756272719839 --cp-ival 1 --score-min L,2.26217277873526,9.86849367563704 --mp 6.1914602617147,3.71891534566311 -R 1 -N 0 -L22 --rfg 43.5392627640801 -q -p 2 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 678s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 678s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '18' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 678s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '24' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 678s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '62' because it was < 2 characters long 678s Warning: skipping mate #2 of read '62' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 678s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #2 of read '66' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 678s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #1 of read '96' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 678s Warning: skipping mate #2 of read '124' because length (1) <= # seed mismatches (0) 678s Warning: skipping mate #2 of read '124' because it was < 2 characters long 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 678s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 678s 147 reads; of these: 678s 147 (100.00%) were paired; of these: 678s 145 (98.64%) aligned concordantly 0 times 678s 0 (0.00%) aligned concordantly exactly 1 time 678s 2 (1.36%) aligned concordantly >1 times 678s ---- 678s 145 pairs aligned concordantly 0 times; of these: 678s 0 (0.00%) aligned discordantly 1 time 678s ---- 678s 145 pairs aligned 0 times concordantly or discordantly; of these: 678s 290 mates make up the pairs; of these: 678s 225 (77.59%) aligned 0 times 678s 42 (14.48%) aligned exactly 1 time 678s 23 (7.93%) aligned >1 times 678s 23.47% overall alignment rate 678s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 678s Flattened IUPAC characters 678s Mutating sequence Sim.pm.2 678s *** Run 76 of 100 678s /usr/bin/bowtie2 --cp-ival 1 -M 3 --trim5 0 --norc --rfg 7.52743609008941,12.4151564199889 --trim3 3 -N 0 -L13 --mp 6.99561792548165,5.30757678167151 --np 4 --cp-min 5 --rdg 11.7398155657036,12.8949007843931 --score-min L,7.48362475266126,2.99868325930465 --ma 31.6095728300576 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 678s Introducing 2 SNPs, 0/0 ref/read gaps, and 3 rearrangements 678s Finished SNPs 678s Finished ref gaps 678s Finished read gaps 678s Mutating sequence Sim.pm.1 678s Introducing 13 SNPs, 1/2 ref/read gaps, and 1 rearrangements 678s Finished SNPs 678s Finished ref gaps 678s Finished read gaps 678s Mutated reference genome to subject genome 678s SNPs introduced: 15 678s Reference gaps introduced: 1 678s Read gaps introduced: 2 678s Rearrangements introduced: 4 678s Created read sampler 678s Sampling 153 reads 678s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 678s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 678s parsing sequence Sim.pm.1... 678s parsing sequence Sim.pm.2... 678s Parsed 143 reference bases 678s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 678s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 679s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 679s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 679s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 679s Read 50 alignments... 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_145_145_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 679s Read 100 alignments... 679s Read 150 alignments... 679s 153 reads; of these: 679s 141 (92.16%) were paired; of these: 679s 139 (98.58%) aligned concordantly 0 times 679s 1 (0.71%) aligned concordantly exactly 1 time 679s 1 (0.71%) aligned concordantly >1 times 679s ---- 679s 139 pairs aligned concordantly 0 times; of these: 679s 1 (0.72%) aligned discordantly 1 time 679s ---- 679s 138 pairs aligned 0 times concordantly or discordantly; of these: 679s 276 mates make up the pairs; of these: 679s 242 (87.68%) aligned 0 times 679s 23 (8.33%) aligned exactly 1 time 679s 11 (3.99%) aligned >1 times 679s 12 (7.84%) were unpaired; of these: 679s 7 (58.33%) aligned 0 times 679s 5 (41.67%) aligned exactly 1 time 679s 0 (0.00%) aligned >1 times 679s 15.31% overall alignment rate 679s Read 200 alignments... 679s Read 250 alignments... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GTG 679s GTG 679s Processing line... 679s Processing line... 679s CT 679s CT 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s ACCGC 679s ACCGC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CTC 679s CTC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCT 679s GTGGTAGGGGGGGACTGGCGGGAAGACCGCGGCT 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GTGGTGTTGAGAG 679s GTGGTGTTGAGAG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CGCC 679s CGCC 679s Processing line... 679s Processing line... 679s Processing line... 679s CGCCC 679s CGCCC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GCGC 679s GCGC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGG 679s GGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s AA 679s AA 679s Processing line... 679s Processing line... 679s CGGG 679s CGGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s ACC 679s ACC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s AGGGAG 679s AGGGAG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGAGGGAGCTG 679s GGAGGGAGCTG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGCTG 679s GGGGGACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGCTG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGGAA 679s GGGAA 679s Processing line... 679s AAGACCGCGGCTCGGT 679s AAGACCGCGGCTCGGT 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CCA 679s CCA 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s AGGG 679s AGGG 679s Processing line... 679s TGCGCCCAGCTTAGGCGGTCAGGAGG 679s TGCGCCCAGCTTAGGCGGTCAGGAGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGTAGGGGGGGACTGGCGGGAAGAC 679s GGTAGGGGGGGACTGGCGGGAAGAC 679s Processing line... 679s GTAGGGGGGG 679s GTAGGGGGGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GCGCCCAGCTTAGGCGGT 679s GCGCCCAGCTTAGGCGGT 679s Processing line... 679s Processing line... 679s CGGTCTGCGCCCAGCTTAGGCGGT 679s CGGTCTGCGCCCAGCTTAGGCGGT 679s Processing line... 679s Processing line... 679s GTCAGGA 679s GTCAGGA 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CTG 679s CTG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GCGGCTCGGTCTGCGCCCAG 679s GCGGCTCGGTCTGCGCCCAG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s TCCGGGTGGTGT 679s TCCGGGTGGTGT 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s AAG 679s AAG 679s Processing line... 679s Processing line... 679s GTGGT 679s GTGGT 679s Processing line... 679s Processing line... 679s GGGAAGACCGCGGCT 679s GGGAAGACCGCGGCT 679s Processing line... 679s Processing line... 679s AA 679s AA 679s Processing line... 679s Processing line... 679s CGCGG 679s CGCGG 679s Processing line... 679s Processing line... 679s GTGTTG 679s GTGTTG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CGGGTGGTGTTGAGAG 679s CGGGTGGTGTTGAGAG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CTGCGCCCAGCTTAGGCGGTCAGGAGGGA 679s CTGCGCCCAGCTTAGGCGGTCAGGAGGGA 679s Processing line... 679s Processing line... 679s AGACCGCGGCTCGGTCTGC 679s AGACCGCGGCTCGGTCTGC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s TGCGCCCAGCTTAGG 679s TGCGCCCAGCTTAGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CCCAGCTTAGGCGGTCAGGAGGGAGC 679s CCCAGCTTAGGCGGTCAGGAGGGAGC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CA 679s CA 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CC 679s CC 679s Processing line... 679s Processing line... 679s Processing line... 679s GT 679s GT 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s ACAG 679s ACAG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GCGCCC 679s GCGCCC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s --- Summary --- 679s Read 1 reference strings 679s Checked 45 alignments, 0 edits 679s --------------- 679s PASSED 679s ALSO checking that bowtie2 and bowtie2-align match up 679s /usr/bin/bowtie2 --cp-ival 1 -M 3 --trim5 0 --norc --rfg 7.52743609008941,12.4151564199889 --trim3 3 -N 0 -L13 --mp 6.99561792548165,5.30757678167151 --np 4 --cp-min 5 --rdg 11.7398155657036,12.8949007843931 --score-min L,7.48362475266126,2.99868325930465 --ma 31.6095728300576 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 679s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 679s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 679s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 679s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 679s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_145_145_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 679s 153 reads; of these: 679s 141 (92.16%) were paired; of these: 679s 139 (98.58%) aligned concordantly 0 times 679s 1 (0.71%) aligned concordantly exactly 1 time 679s 1 (0.71%) aligned concordantly >1 times 679s ---- 679s 139 pairs aligned concordantly 0 times; of these: 679s 1 (0.72%) aligned discordantly 1 time 679s ---- 679s 138 pairs aligned 0 times concordantly or discordantly; of these: 679s 276 mates make up the pairs; of these: 679s 242 (87.68%) aligned 0 times 679s 23 (8.33%) aligned exactly 1 time 679s 11 (3.99%) aligned >1 times 679s 12 (7.84%) were unpaired; of these: 679s 7 (58.33%) aligned 0 times 679s 5 (41.67%) aligned exactly 1 time 679s 0 (0.00%) aligned >1 times 679s 15.31% overall alignment rate 679s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 679s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 679s /usr/bin/bowtie2 --cp-ival 1 -M 3 --trim5 0 --norc --rfg 7.52743609008941,12.4151564199889 --trim3 3 -N 0 -L13 --mp 6.99561792548165,5.30757678167151 --np 4 --cp-min 5 --rdg 11.7398155657036,12.8949007843931 --score-min L,7.48362475266126,2.99868325930465 --ma 31.6095728300576 --qseq -p 2 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 679s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 679s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 679s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 679s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 679s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_145_145_1/1' because length (0) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 679s 153 reads; of these: 679s 141 (92.16%) were paired; of these: 679s 139 (98.58%) aligned concordantly 0 times 679s 1 (0.71%) aligned concordantly exactly 1 time 679s 1 (0.71%) aligned concordantly >1 times 679s ---- 679s 139 pairs aligned concordantly 0 times; of these: 679s 1 (0.72%) aligned discordantly 1 time 679s ---- 679s 138 pairs aligned 0 times concordantly or discordantly; of these: 679s 276 mates make up the pairs; of these: 679s 242 (87.68%) aligned 0 times 679s 23 (8.33%) aligned exactly 1 time 679s 11 (3.99%) aligned >1 times 679s 12 (7.84%) were unpaired; of these: 679s 7 (58.33%) aligned 0 times 679s 5 (41.67%) aligned exactly 1 time 679s 0 (0.00%) aligned >1 times 679s 15.31% overall alignment rate 679s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 679s Flattened IUPAC characters 679s Mutating sequence Sim.pm.1 679s Introducing 1 SNPs, 4/1 ref/read gaps, and 0 rearrangements 679s Finished SNPs 679s Finished ref gaps 679s Finished read gaps 679s Mutating sequence Sim.pm.2 679s Introducing 3 SNPs, 1/1 ref/read gaps, and 5 rearrangements 679s Finished SNPs 679s Finished ref gaps 679s Finished read gaps 679s Mutated reference genome to subject genome 679s SNPs introduced: 4 679s Reference gaps introduced: 5 679s Read gaps introduced: 2 679s Rearrangements introduced: 5 679s Created read sampler 679s Sampling 134 reads 679s *** Run 77 of 100 679s /usr/bin/bowtie2 --cp-ival 1 --np 4 --cp-min 3 --n-ceil 1.21095854855677,0.222182960661851 --mm --rfg 44.288646160874 --score-min L,2.42810643063348,6.63237758854036 --mp 7.45163596812126,3.53109334602157 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 679s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 679s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 679s parsing sequence Sim.pm.1... 679s parsing sequence Sim.pm.2... 679s Parsed 143 reference bases 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 679s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 679s Warning: skipping mate #2 of read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 679s Read 50 alignments... 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 679s Read 100 alignments... 679s Read 150 alignments... 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 679s Warning: skipping mate #2 of read 'R_1_1_1_125_125_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 679s 134 reads; of these: 679s 134 (100.00%) were paired; of these: 679s 130 (97.01%) aligned concordantly 0 times 679s 3 (2.24%) aligned concordantly exactly 1 time 679s 1 (0.75%) aligned concordantly >1 times 679s ---- 679s 130 pairs aligned concordantly 0 times; of these: 679s 2 (1.54%) aligned discordantly 1 time 679s ---- 679s 128 pairs aligned 0 times concordantly or discordantly; of these: 679s 256 mates make up the pairs; of these: 679s 210 (82.03%) aligned 0 times 679s 26 (10.16%) aligned exactly 1 time 679s 20 (7.81%) aligned >1 times 679s 21.64% overall alignment rate 679s Read 200 alignments... 679s Read 250 alignments... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s TGGCGGGAAGACCGCG 679s TGGCGGGAAGACCGCG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGGTGG 679s GGGTGG 679s Processing line... 679s Processing line... 679s GTGTTG 679s GTGTTG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GAG 679s GAG 679s Processing line... 679s Processing line... 679s CGCCCAGCTTAGG 679s CGCCCAGCTTAGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GG 679s GG 679s Processing line... 679s Processing line... 679s GGGAAGACCGCGGCTC 679s GGGAAGACCGCGGCTC 679s Processing line... 679s Processing line... 679s CT 679s CT 679s Processing line... 679s Processing line... 679s GTT 679s GTT 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GAC 679s GAC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CG 679s CG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CGGTCTGCGCCC 679s CGGTCTGCGCCC 679s Processing line... 679s Processing line... 679s TGGTAGGGGG 679s TGGTAGGGGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CTCGGTCTGCGCCCAGCTT 679s CTCGGTCTGCGCCCAGCTT 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GTTGA 679s GTTGA 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s TT 679s TT 679s Processing line... 679s /usr/bin/bowtie2 --cp-ival 1 --np 4 --cp-min 3 --n-ceil 1.21095854855677,0.222182960661851 --mm --rfg 44.288646160874 --score-min L,2.42810643063348,6.63237758854036 --mp 7.45163596812126,3.53109334602157 --qseq -p 2 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 679s Processing line... 679s Processing line... 679s Processing line... 679s TGGTGGTGGTAG 679s TGGTGGTGGTAG 679s Processing line... 679s Processing line... 679s CTGCGCCCAGCTTAGGCGGTCAGGAGG 679s CTGCGCCCAGCTTAGGCGGTCAGGAGG 679s Processing line... 679s Processing line... 679s AG 679s AG 679s Processing line... 679s Processing line... 679s GAA 679s GAA 679s Processing line... 679s GGTAGGGGGGG 679s GGTAGGGGGGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGT 679s GGT 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGTGA 679s GGTGA 679s Processing line... 679s Processing line... 679s GGTGGTGTTGAGAGGGTGACAGA 679s GGTGGTGTTGAGAGGGTGACAGA 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s AGGCGGTCAG 679s AGGCGGTCAG 679s Processing line... 679s Processing line... 679s TAGG 679s TAGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s ACCGCGGCTCGGTC 679s ACCGCGGCTCGGTC 679s Processing line... 679s CGGGAAGACCGCGGCTCGGTCTGCGCCCAGCT 679s CGGGAAGACCGCGGCTCGGTCTGCGCCCAGCT 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGCGGGAAGACCG 679s GGCGGGAAGACCG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CTGCGCCCAGCTTAGGCGGTCAGGAGGG 679s CTGCGCCCAGCTTAGGCGGTCAGGAGGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CCCAGC 679s CCCAGC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GT 679s GT 679s Processing line... 679s Processing line... 679s GTAGGGGGGGACTGGCGG 679s GTAGGGGGGGACTGGCGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGA 679s GGA 679s Processing line... 679s AGAGGCGTGG 679s AGAGGCGTGG 679s Processing line... 679s Processing line... 679s Processing line... 679s GTCTGCGCCCAGCTTAGG 679s GTCTGCGCCCAGCTTAGG 679s Processing line... 679s Processing line... 679s TAGG 679s TAGG 679s Processing line... 679s Processing line... 679s GACTGGCGG 679s GACTGGCGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGGAAGACCGCGGCTCG 679s GGGAAGACCGCGGCTCG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGTGGTAGGGGGGGACTGGCGGGAAGAC 679s GGTGGTAGGGGGGGACTGGCGGGAAGAC 679s Processing line... 679s TTAGGC 679s TTAGGC 679s Processing line... 679s GTG 679s GTG 679s Processing line... 679s Processing line... 679s GACCGCGGCT 679s GACCGCGGCT 679s Processing line... 679s GCGGCTCGGTCTGCGC 679s GCGGCTCGGTCTGCGC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GTCAG 679s GTCAG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GCCCAGCTTAGGCGGTCAG 679s GCCCAGCTTAGGCGGTCAG 679s Processing line... 679s GACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAG 679s GACTGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAG 679s Processing line... 679s AGGGTGAC 679s AGGGTGAC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s CGGCTCGGTCTGCGCCCAGCTT 679s CGGCTCGGTCTGCGCCCAGCTT 679s Processing line... 679s Processing line... 679s GG 679s GG 679s Processing line... 679s CTCGGTCTGCGCCCAGC 679s CTCGGTCTGCGCCCAGC 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s AGGAGGGAGCT 679s AGGAGGGAGCT 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGG 679s GGG 679s Processing line... 679s Processing line... 679s GGGTGGTGTTGAGAGGGTGACAGA 679s GGGTGGTGTTGAGAGGGTGACAGA 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GGACTG 679s GGACTG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s GC 679s GC 679s Processing line... 679s Processing line... 679s TGC 679s TGC 679s Processing line... 679s Processing line... 679s GGTGGTGGTAGGGG 679s GGTGGTGGTAGGGG 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s --- Summary --- 679s Read 1 reference strings 679s Checked 58 alignments, 0 edits 679s --------------- 679s PASSED 679s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 679s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 679s Warning: skipping mate #2 of read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 679s Warning: skipping mate #2 of read 'R_1_1_1_125_125_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #2 of read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 679s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (1) <= # seed mismatches (0) 679s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 679s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 679s 134 reads; of these: 679s 134 (100.00%) were paired; of these: 679s 130 (97.01%) aligned concordantly 0 times 679s 3 (2.24%) aligned concordantly exactly 1 time 679s 1 (0.75%) aligned concordantly >1 times 679s ---- 679s 130 pairs aligned concordantly 0 times; of these: 679s 2 (1.54%) aligned discordantly 1 time 679s ---- 679s 128 pairs aligned 0 times concordantly or discordantly; of these: 679s 256 mates make up the pairs; of these: 679s 210 (82.03%) aligned 0 times 679s 26 (10.16%) aligned exactly 1 time 679s 20 (7.81%) aligned >1 times 679s 21.64% overall alignment rate 679s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 679s Flattened IUPAC characters 679s Mutating sequence Sim.pm.2 679s Introducing 9 SNPs, 1/0 ref/read gaps, and 0 rearrangements 679s Finished SNPs 679s Finished ref gaps 679s Finished read gaps 679s Mutating sequence Sim.pm.1 679s Introducing 4 SNPs, 0/4 ref/read gaps, and 1 rearrangements 679s Finished SNPs 679s Finished ref gaps 679s Finished read gaps 679s Mutated reference genome to subject genome 679s SNPs introduced: 13 679s Reference gaps introduced: 1 679s Read gaps introduced: 4 679s Rearrangements introduced: 1 679s Created read sampler 679s Sampling 61 reads 679s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 679s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 679s parsing sequence Sim.pm.1... 679s parsing sequence Sim.pm.2... 679s Parsed 143 reference bases 679s *** Run 78 of 100 679s /usr/bin/bowtie2 --cp-ival 1 --local --norc --cp-min 7 -M 3 --rfg 29.665882409364 --mm -R 2 --score-min L,1.56554349980838,6.36592008224838 -q -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq 679s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 679s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 679s Warning: skipping read '18' because it was < 2 characters long 679s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 679s Warning: skipping read '33' because it was < 2 characters long 679s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 679s Warning: skipping read '42' because it was < 2 characters long 679s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 679s Warning: skipping read '43' because it was < 2 characters long 679s 61 reads; of these: 679s 61 (100.00%) were unpaired; of these: 679s 61 (100.00%) aligned 0 times 679s 0 (0.00%) aligned exactly 1 time 679s 0 (0.00%) aligned >1 times 679s 0.00% overall alignment rate 679s Read 50 alignments... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s Processing line... 679s --- Summary --- 679s Read 1 reference strings 679s Checked 0 alignments, 0 edits 679s --------------- 679s PASSED 679s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 679s /usr/bin/bowtie2 --cp-ival 1 --local --norc --cp-min 7 -M 3 --rfg 29.665882409364 --mm -R 2 --score-min L,1.56554349980838,6.36592008224838 -q -p 4 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 679s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 679s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 679s Warning: skipping read '18' because it was < 2 characters long 679s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 679s Warning: skipping read '33' because it was < 2 characters long 679s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 679s Warning: skipping read '42' because it was < 2 characters long 679s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 679s Warning: skipping read '43' because it was < 2 characters long 680s 61 reads; of these: 680s 61 (100.00%) were unpaired; of these: 680s 61 (100.00%) aligned 0 times 680s 0 (0.00%) aligned exactly 1 time 680s 0 (0.00%) aligned >1 times 680s 0.00% overall alignment rate 680s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 680s Flattened IUPAC characters 680s Mutating sequence Sim.pm.2 680s Introducing 15 SNPs, 1/0 ref/read gaps, and 0 rearrangements 680s Finished SNPs 680s Finished ref gaps 680s Finished read gaps 680s Mutating sequence Sim.pm.1 680s Introducing 6 SNPs, 1/0 ref/read gaps, and 3 rearrangements 680s Finished SNPs 680s Finished ref gaps 680s Finished read gaps 680s Mutated reference genome to subject genome 680s SNPs introduced: 21 680s Reference gaps introduced: 2 680s Read gaps introduced: 0 680s Rearrangements introduced: 3 680s Created read sampler 680s Sampling 113 reads 680s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 680s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 680s parsing sequence Sim.pm.1... 680s parsing sequence Sim.pm.2... 680s Parsed 143 reference bases 680s *** Run 79 of 100 680s /usr/bin/bowtie2 --ma 10.1227850725114 --score-min L,9.97961020668357,7.53766661030318 -R 4 --mp 4.97259151035467,3.03665916207993 --gbar 2 --cp-ival 2 --np 2 --cp-min 7 -M 3 -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw 680s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 680s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 680s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 680s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 680s Warning: skipping read '33' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 680s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 680s Warning: skipping read '76' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 680s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 680s Warning: skipping read '79' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 680s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 680s Warning: skipping read '93' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 680s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 680s Warning: skipping read '95' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 680s 113 reads; of these: 680s 113 (100.00%) were unpaired; of these: 680s 89 (78.76%) aligned 0 times 680s 8 (7.08%) aligned exactly 1 time 680s 16 (14.16%) aligned >1 times 680s 21.24% overall alignment rate 680s Read 50 alignments... 680s Read 100 alignments... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GT 680s GT 680s Processing line... 680s CGTG 680s CGTG 680s Processing line... 680s CGTGG 680s CGTGG 680s Processing line... 680s Processing line... 680s Processing line... 680s TGGTGGTGGTAGGGGGG 680s TGGTGGTGGTAGGGGGG 680s Processing line... 680s Processing line... 680s GCC 680s GCC 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TGACA 680s TGACA 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TGAC 680s TGAC 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GAAGAC 680s GAAGAC 680s Processing line... 680s Processing line... 680s GCG 680s GCG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GAA 680s GAA 680s Processing line... 680s GGT 680s GGT 680s Processing line... 680s Processing line... 680s Processing line... 680s ACTGGC 680s ACTGGC 680s Processing line... 680s Processing line... 680s GAGG 680s GAGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s /usr/bin/bowtie2 --ma 10.1227850725114 --score-min L,9.97961020668357,7.53766661030318 -R 4 --mp 4.97259151035467,3.03665916207993 --gbar 2 --cp-ival 2 --np 2 --cp-min 7 -M 3 -r -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GG 680s GG 680s Processing line... 680s Processing line... 680s Processing line... 680s CGGTCAGG 680s CGGTCAGG 680s Processing line... 680s TTAGGCGGTCAGGAGGG 680s TTAGGCGGTCAGGAGGG 680s Processing line... 680s GTG 680s GTG 680s Processing line... 680s Processing line... 680s Processing line... 680s GT 680s GT 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s CGTG 680s CGTG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GGCGTG 680s GGCGTG 680s Processing line... 680s Processing line... 680s Processing line... 680s GGG 680s GGG 680s Processing line... 680s Processing line... 680s GTGGTA 680s GTGGTA 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s AGG 680s AGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GGTG 680s GGTG 680s Processing line... 680s Processing line... 680s Processing line... 680s --- Summary --- 680s Read 1 reference strings 680s Checked 24 alignments, 0 edits 680s --------------- 680s PASSED 680s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 680s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 680s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 680s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 680s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 680s Warning: skipping read '33' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 680s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 680s Warning: skipping read '76' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 680s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 680s Warning: skipping read '79' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 680s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 680s Warning: skipping read '93' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 680s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 680s Warning: skipping read '95' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 680s 113 reads; of these: 680s 113 (100.00%) were unpaired; of these: 680s 89 (78.76%) aligned 0 times 680s 8 (7.08%) aligned exactly 1 time 680s 16 (14.16%) aligned >1 times 680s 21.24% overall alignment rate 680s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 680s Flattened IUPAC characters 680s Mutating sequence Sim.pm.1 680s Introducing 5 SNPs, 1/2 ref/read gaps, and 0 rearrangements 680s Finished SNPs 680s Finished ref gaps 680s Finished read gaps 680s Mutating sequence Sim.pm.2 680s Introducing 2 SNPs, 1/0 ref/read gaps, and 3 rearrangements 680s Finished SNPs 680s Finished ref gaps 680s Finished read gaps 680s Mutated reference genome to subject genome 680s SNPs introduced: 7 680s Reference gaps introduced: 2 680s Read gaps introduced: 2 680s Rearrangements introduced: 3 680s Created read sampler 680s Sampling 187 reads 680s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 680s *** Run 80 of 100 680s /usr/bin/bowtie2 -a --np 2 --cp-min 2 --cp-ival 1 --mp 8.51316264440251,4.16709854230442 --score-min L,2.19595279482007,2.51032500405685 --trim3 3 --rdg 23.1289396076276 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 680s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 680s parsing sequence Sim.pm.1... 680s parsing sequence Sim.pm.2... 680s Parsed 143 reference bases 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 680s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 680s Warning: skipping mate #2 of read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #2 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 680s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 680s Read 50 alignments... 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 680s Warning: skipping mate #2 of read 'R_1_1_1_95_95_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #2 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 680s Warning: skipping mate #2 of read 'R_1_1_1_100_100_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #2 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_145_145_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 680s Read 100 alignments... 680s Read 150 alignments... 680s Read 200 alignments... 680s Read 250 alignments... 680s Read 300 alignments... 680s Read 350 alignments... 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_152_152_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_152_152_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 680s Read 400 alignments... 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_162_162_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_162_162_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_169_169_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_169_169_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 680s Warning: skipping mate #2 of read 'R_1_1_1_170_170_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #2 of read 'R_1_1_1_170_170_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_174_174_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_174_174_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_176_176_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_176_176_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_178_178_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_178_178_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_182_182_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_182_182_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_183_183_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_183_183_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_184_184_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_184_184_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_185_185_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_185_185_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_186_186_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_186_186_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_187_187_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_187_187_1/1; setting to 0 instead 680s 187 reads; of these: 680s 181 (96.79%) were paired; of these: 680s 176 (97.24%) aligned concordantly 0 times 680s 2 (1.10%) aligned concordantly exactly 1 time 680s 3 (1.66%) aligned concordantly >1 times 680s ---- 680s 176 pairs aligned concordantly 0 times; of these: 680s 5 (2.84%) aligned discordantly 1 time 680s ---- 680s 171 pairs aligned 0 times concordantly or discordantly; of these: 680s 342 mates make up the pairs; of these: 680s 283 (82.75%) aligned 0 times 680s 41 (11.99%) aligned exactly 1 time 680s 18 (5.26%) aligned >1 times 680s 6 (3.21%) were unpaired; of these: 680s 4 (66.67%) aligned 0 times 680s 2 (33.33%) aligned exactly 1 time 680s 0 (0.00%) aligned >1 times 680s 22.01% overall alignment rate 680s Read 450 alignments... 680s Read 500 alignments... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GGCTCGGTCTGCG 680s GGCTCGGTCTGCG 680s Processing line... 680s TGCGCCCAGCTTAGGCGGT 680s TGCGCCCAGCTTAGGCGGT 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s CCGCGGCTCGGT 680s CCGCGGCTCGGT 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GCGGC 680s GCGGC 680s Processing line... 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s CA 680s CA 680s Processing line... 680s TG 680s TG 680s Processing line... 680s CA 680s CA 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s CA 680s CA 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s Processing line... 680s Processing line... 680s CGGCTC 680s CGGCTC 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s ACTGGCGGG 680s ACTGGCGGG 680s Processing line... 680s ACTGGCGGGAAGACCGCG 680s ACTGGCGGGAAGACCGCG 680s Processing line... 680s CGGTCA 680s CGGTCA 680s Processing line... 680s GGTAGGGGGGGACTGGCGG 680s GGTAGGGGGGGACTGGCGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GT 680s GT 680s Processing line... 680s AC 680s AC 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s AC 680s AC 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s AC 680s AC 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GGCGG 680s GGCGG 680s Processing line... 680s GGCGG 680s GGCGG 680s Processing line... 680s Processing line... 680s GCGGC 680s GCGGC 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s AGGA 680s AGGA 680s Processing line... 680s Processing line... 680s GGTGTTGAGAGGGTGA 680s GGTGTTGAGAGGGTGA 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TCCGGGTGGTGTTGAGAGGG 680s TCCGGGTGGTGTTGAGAGGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GTGGTGGTAGGGGG 680s GTGGTGGTAGGGGG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s CC 680s CC 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s CC 680s CC 680s Processing line... 680s GG 680s GG 680s Processing line... 680s CC 680s CC 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s CC 680s CC 680s Processing line... 680s CC 680s CC 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TCTGCGCCCAGCTTAGG 680s TCTGCGCCCAGCTTAGG 680s Processing line... 680s GGGAGC 680s GGGAGC 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s AC 680s AC 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s AC 680s AC 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s AC 680s AC 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s GT 680s GT 680s Processing line... 680s Processing line... 680s GGGGGAC 680s GGGGGAC 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TG 680s TG 680s Processing line... 680s CA 680s CA 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s CA 680s CA 680s Processing line... 680s TG 680s TG 680s Processing line... 680s TG 680s TG 680s Processing line... 680s CA 680s CA 680s Processing line... 680s TG 680s TG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TGGTGTTG 680s TGGTGTTG 680s Processing line... 680s TGGTGTTG 680s TGGTGTTG 680s Processing line... 680s Processing line... 680s GGGTGACAGAGG 680s GGGTGACAGAGG 680s Processing line... 680s Processing line... 680s CGT 680s CGT 680s Processing line... 680s CGT 680s CGT 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GTCTGCGCCCAGCTTAGGCGGTCA 680s GTCTGCGCCCAGCTTAGGCGGTCA 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TGCGCCCAGCT 680s TGCGCCCAGCT 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GGGACTGGC 680s GGGACTGGC 680s Processing line... 680s Processing line... 680s GTCAGG 680s GTCAGG 680s Processing line... 680s Processing line... 680s GGGAC 680s GGGAC 680s Processing line... 680s GCT 680s GCT 680s Processing line... 680s GCT 680s GCT 680s Processing line... 680s AGC 680s AGC 680s Processing line... 680s GCT 680s GCT 680s Processing line... 680s AGC 680s AGC 680s Processing line... 680s TGAC 680s TGAC 680s Processing line... 680s GTCA 680s GTCA 680s Processing line... 680s Processing line... 680s GACA 680s GACA 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s AGGGGGG 680s AGGGGGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GGAGGG 680s GGAGGG 680s Processing line... 680s GG 680s GG 680s Processing line... 680s GGAGGG 680s GGAGGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TCTG 680s TCTG 680s Processing line... 680s CAGA 680s CAGA 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s AGG 680s AGG 680s Processing line... 680s AGG 680s AGG 680s Processing line... 680s AGG 680s AGG 680s Processing line... 680s AGG 680s AGG 680s Processing line... 680s AGG 680s AGG 680s Processing line... 680s AGG 680s AGG 680s Processing line... 680s AGG 680s AGG 680s Processing line... 680s Processing line... 680s CCCAGCTTAGGCGGT 680s CCCAGCTTAGGCGGT 680s Processing line... 680s Processing line... 680s GGTGTTGAGA 680s GGTGTTGAGA 680s Processing line... 680s Processing line... 680s CCCAGCTTAGGCGGTCAGG 680s CCCAGCTTAGGCGGTCAGG 680s Processing line... 680s GCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAG 680s GCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s AGAGGGTGACAG 680s AGAGGGTGACAG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s CGGTCAGGAGGGAGCT 680s CGGTCAGGAGGGAGCT 680s Processing line... 680s CCGC 680s CCGC 680s Processing line... 680s GCGG 680s GCGG 680s Processing line... 680s GCGG 680s GCGG 680s Processing line... 680s GCGG 680s GCGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GGTGGTGTTGAGAGGGTGACAGA 680s GGTGGTGTTGAGAGGGTGACAGA 680s Processing line... 680s Processing line... 680s AGCTTAGGC 680s AGCTTAGGC 680s Processing line... 680s Processing line... 680s CGCGGCTCGGTC 680s CGCGGCTCGGTC 680s Processing line... 680s Processing line... 680s GGTGGTGGTA 680s GGTGGTGGTA 680s Processing line... 680s ACCGCGGCTCG 680s ACCGCGGCTCG 680s Processing line... 680s GTAGGGGGGGACTGGCGGGAAGACCGC 680s GTAGGGGGGGACTGGCGGGAAGACCGC 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGG 680s TGGCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GCCCAGCTTAGGCGGTCAG 680s GCCCAGCTTAGGCGGTCAG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s CGGGTGGTGTTGAGAGGGTGACAGAGGCGTG 680s CGGGTGGTGTTGAGAGGGTGACAGAGGCGTG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GGCTCGGTCTGCGCCCAG 680s GGCTCGGTCTGCGCCCAG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TG 680s TG 680s Processing line... 680s ACA 680s ACA 680s Processing line... 680s TG 680s TG 680s Processing line... 680s ACA 680s ACA 680s Processing line... 680s CA 680s CA 680s Processing line... 680s TGT 680s TGT 680s Processing line... 680s TG 680s TG 680s Processing line... 680s ACA 680s ACA 680s Processing line... 680s TG 680s TG 680s Processing line... 680s ACA 680s ACA 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TGACAGAGGCGTG 680s TGACAGAGGCGTG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s /usr/bin/bowtie2 -a --np 2 --cp-min 2 --cp-ival 1 --mp 8.51316264440251,4.16709854230442 --score-min L,2.19595279482007,2.51032500405685 --trim3 3 --rdg 23.1289396076276 --qseq -p 4 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 680s Processing line... 680s CCCAGCTTAGGCGGTCAG 680s CCCAGCTTAGGCGGTCAG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s AGGA 680s AGGA 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GAGAG 680s GAGAG 680s Processing line... 680s Processing line... 680s Processing line... 680s GGGGGGGACTGGCGGGAAGACC 680s GGGGGGGACTGGCGGGAAGACC 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TGCG 680s TGCG 680s Processing line... 680s Processing line... 680s CGTGG 680s CGTGG 680s Processing line... 680s CGTGG 680s CGTGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GGTAGGGGGGGACTGGCGGGAAGACC 680s GGTAGGGGGGGACTGGCGGGAAGACC 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GTAGGGGGGGACTGG 680s GTAGGGGGGGACTGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TGGT 680s TGGT 680s Processing line... 680s TGGT 680s TGGT 680s Processing line... 680s TGGT 680s TGGT 680s Processing line... 680s TGGT 680s TGGT 680s Processing line... 680s TGGT 680s TGGT 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s CGGTCTGCGCCCA 680s CGGTCTGCGCCCA 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GGGAAGACCGCGG 680s GGGAAGACCGCGG 680s Processing line... 680s Processing line... 680s AGGCG 680s AGGCG 680s Processing line... 680s GTGTTGAGAGGG 680s GTGTTGAGAGGG 680s Processing line... 680s CCGGGTGGTGTTGA 680s CCGGGTGGTGTTGA 680s Processing line... 680s CCGGGTGGTGTTGA 680s CCGGGTGGTGTTGA 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GTTGAGAGGG 680s GTTGAGAGGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s CGGCTCGGTCTGCGCCCAGCTT 680s CGGCTCGGTCTGCGCCCAGCTT 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TTG 680s TTG 680s Processing line... 680s TTG 680s TTG 680s Processing line... 680s Processing line... 680s TGGTGGTAGGGGGGGACTGGCGGGAAGA 680s TGGTGGTAGGGGGGGACTGGCGGGAAGA 680s Processing line... 680s GCGGCTCGGTCTGC 680s GCGGCTCGGTCTGC 680s Processing line... 680s Processing line... 680s Processing line... 680s GTG 680s GTG 680s Processing line... 680s GTG 680s GTG 680s Processing line... 680s GTG 680s GTG 680s Processing line... 680s GTG 680s GTG 680s Processing line... 680s GTG 680s GTG 680s Processing line... 680s GTG 680s GTG 680s Processing line... 680s GTG 680s GTG 680s Processing line... 680s GTG 680s GTG 680s Processing line... 680s GTG 680s GTG 680s Processing line... 680s GGGGGA 680s GGGGGA 680s Processing line... 680s Processing line... 680s Processing line... 680s AAGACCG 680s AAGACCG 680s Processing line... 680s --- Summary --- 680s Read 1 reference strings 680s Checked 226 alignments, 0 edits 680s --------------- 680s PASSED 680s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 680s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 680s Warning: skipping mate #2 of read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #2 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 680s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 680s Warning: skipping mate #2 of read 'R_1_1_1_95_95_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #2 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 680s Warning: skipping mate #2 of read 'R_1_1_1_100_100_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #2 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_145_145_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_162_162_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_162_162_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_169_169_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_169_169_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 680s Warning: skipping mate #2 of read 'R_1_1_1_170_170_1/1' because length (1) <= # seed mismatches (0) 680s Warning: skipping mate #2 of read 'R_1_1_1_170_170_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_174_174_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_174_174_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_176_176_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_176_176_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_152_152_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_152_152_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 680s Warning: skipping mate #1 of read 'R_1_1_1_178_178_1/1' because length (0) <= # seed mismatches (0) 680s Warning: skipping mate #1 of read 'R_1_1_1_178_178_1/1' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_182_182_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_182_182_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_183_183_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_183_183_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_184_184_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_184_184_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_185_185_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_185_185_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_186_186_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_186_186_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_187_187_1/1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_187_187_1/1; setting to 0 instead 680s 187 reads; of these: 680s 181 (96.79%) were paired; of these: 680s 176 (97.24%) aligned concordantly 0 times 680s 2 (1.10%) aligned concordantly exactly 1 time 680s 3 (1.66%) aligned concordantly >1 times 680s ---- 680s 176 pairs aligned concordantly 0 times; of these: 680s 5 (2.84%) aligned discordantly 1 time 680s ---- 680s 171 pairs aligned 0 times concordantly or discordantly; of these: 680s 342 mates make up the pairs; of these: 680s 283 (82.75%) aligned 0 times 680s 41 (11.99%) aligned exactly 1 time 680s 18 (5.26%) aligned >1 times 680s 6 (3.21%) were unpaired; of these: 680s 4 (66.67%) aligned 0 times 680s 2 (33.33%) aligned exactly 1 time 680s 0 (0.00%) aligned >1 times 680s 22.01% overall alignment rate 680s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 680s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 680s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 680s Flattened IUPAC characters 680s Mutating sequence Sim.pm.1 680s Introducing 13 SNPs, 0/1 ref/read gaps, and 0 rearrangements 680s Finished SNPs 680s Finished ref gaps 680s Finished read gaps 680s Mutating sequence Sim.pm.2 680s Introducing 8 SNPs, 3/0 ref/read gaps, and 1 rearrangements 680s Finished SNPs 680s Finished ref gaps 680s Finished read gaps 680s Mutated reference genome to subject genome 680s SNPs introduced: 21 680s Reference gaps introduced: 3 680s Read gaps introduced: 1 680s Rearrangements introduced: 1 680s Created read sampler 680s Sampling 84 reads 680s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 680s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 680s parsing sequence Sim.pm.1... 680s parsing sequence Sim.pm.2... 680s Parsed 143 reference bases 680s *** Run 81 of 100 680s /usr/bin/bowtie2 --trim5 6 --cp-ival 1 --nofw --trim3 4 --mp 6.345186484205,1.73183236839518 -i L,0.0945852264015676,0.722894702780084 -N 1 -L20 --rfg 46.5383292016378,18.1805077462192 --cp-min 3 --np 8 --score-min L,4.18609323483795,4.33713038342823 --rdg 36.2389691426942,19.1471400519399 --mm -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 680s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 680s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 680s Warning: skipping read '5' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 680s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '11' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 680s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (1) 680s Warning: skipping mate #2 of read '12' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 680s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '14' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 680s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '18' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 680s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '24' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 680s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '32' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 680s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '34' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 680s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '36' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 680s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 680s Warning: skipping read '39' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 680s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 680s Warning: skipping read '40' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 680s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '43' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 680s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '45' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 680s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '47' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 680s Warning: skipping read '49' because length (1) <= # seed mismatches (1) 680s Warning: skipping read '49' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 680s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '51' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 680s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '55' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 680s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '57' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 680s Warning: skipping read '64' because length (0) <= # seed mismatches (1) 680s Warning: skipping read '64' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 680s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '68' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 680s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 680s Warning: skipping read '75' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 680s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (1) 680s Warning: skipping mate #2 of read '76' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 680s Read 50 alignments... 680s Read 100 alignments... 680s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 680s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '82' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 680s 84 reads; of these: 680s 62 (73.81%) were paired; of these: 680s 62 (100.00%) aligned concordantly 0 times 680s 0 (0.00%) aligned concordantly exactly 1 time 680s /usr/bin/bowtie2 --trim5 6 --cp-ival 1 --nofw --trim3 4 --mp 6.345186484205,1.73183236839518 -i L,0.0945852264015676,0.722894702780084 -N 1 -L20 --rfg 46.5383292016378,18.1805077462192 --cp-min 3 --np 8 --score-min L,4.18609323483795,4.33713038342823 --rdg 36.2389691426942,19.1471400519399 --mm -q -p 4 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 680s 0 (0.00%) aligned concordantly >1 times 680s ---- 680s 62 pairs aligned concordantly 0 times; of these: 680s 0 (0.00%) aligned discordantly 1 time 680s ---- 680s 62 pairs aligned 0 times concordantly or discordantly; of these: 680s 124 mates make up the pairs; of these: 680s 120 (96.77%) aligned 0 times 680s 2 (1.61%) aligned exactly 1 time 680s 2 (1.61%) aligned >1 times 680s 22 (26.19%) were unpaired; of these: 680s 18 (81.82%) aligned 0 times 680s 3 (13.64%) aligned exactly 1 time 680s 1 (4.55%) aligned >1 times 680s 5.48% overall alignment rate 680s Read 150 alignments... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s CTTAG 680s CTTAG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s CGCGGC 680s CGCGGC 680s Processing line... 680s CT 680s CT 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s CTGG 680s CTGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GGTCTGCGCCCAGCTTAGGCGG 680s GGTCTGCGCCCAGCTTAGGCGG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s TTAGGC 680s TTAGGC 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s GGGTG 680s GGGTG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s ACAG 680s ACAG 680s Processing line... 680s Processing line... 680s Processing line... 680s Processing line... 680s --- Summary --- 680s Read 1 reference strings 680s Checked 8 alignments, 0 edits 680s --------------- 680s PASSED 680s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 680s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 680s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 680s Warning: skipping read '5' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 680s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '11' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 680s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (1) 680s Warning: skipping mate #2 of read '12' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 680s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '14' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 680s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '18' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 680s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '24' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 680s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '32' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 680s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '34' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 680s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '36' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 680s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 680s Warning: skipping read '39' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 680s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 680s Warning: skipping read '40' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 680s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '43' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 680s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '45' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 680s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '47' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 680s Warning: skipping read '49' because length (1) <= # seed mismatches (1) 680s Warning: skipping read '49' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 680s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '51' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 680s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '55' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 680s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '57' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 680s Warning: skipping read '64' because length (0) <= # seed mismatches (1) 680s Warning: skipping read '64' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 680s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '68' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 680s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 680s Warning: skipping read '75' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 680s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (1) 680s Warning: skipping mate #2 of read '76' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 680s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (1) 680s Warning: skipping mate #1 of read '82' because it was < 2 characters long 680s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 680s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 680s 84 reads; of these: 680s 62 (73.81%) were paired; of these: 680s 62 (100.00%) aligned concordantly 0 times 680s 0 (0.00%) aligned concordantly exactly 1 time 680s 0 (0.00%) aligned concordantly >1 times 680s ---- 680s 62 pairs aligned concordantly 0 times; of these: 680s 0 (0.00%) aligned discordantly 1 time 680s ---- 680s 62 pairs aligned 0 times concordantly or discordantly; of these: 680s 124 mates make up the pairs; of these: 680s 120 (96.77%) aligned 0 times 680s 2 (1.61%) aligned exactly 1 time 680s 2 (1.61%) aligned >1 times 680s 22 (26.19%) were unpaired; of these: 680s 18 (81.82%) aligned 0 times 680s 3 (13.64%) aligned exactly 1 time 680s 1 (4.55%) aligned >1 times 680s 5.48% overall alignment rate 680s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 680s Flattened IUPAC characters 680s Mutating sequence Sim.pm.1 680s Introducing 23 SNPs, 2/0 ref/read gaps, and 0 rearrangements 680s Finished SNPs 680s Finished ref gaps 680s Finished read gaps 680s Mutating sequence Sim.pm.2 680s Introducing 13 SNPs, 1/0 ref/read gaps, and 0 rearrangements 680s Finished SNPs 680s Finished ref gaps 680s Finished read gaps 680s Mutated reference genome to subject genome 680s SNPs introduced: 36 680s Reference gaps introduced: 3 680s Read gaps introduced: 0 680s Rearrangements introduced: 0 680s Created read sampler 680s Sampling 63 reads 680s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 680s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 680s parsing sequence Sim.pm.1... 680s parsing sequence Sim.pm.2... 680s Parsed 143 reference bases 680s *** Run 82 of 100 680s /usr/bin/bowtie2 --ma 34.3867470570251 --score-min L,2.99664466721695,3.73640098543562 -k 2 --rfg 24.3457038008537,6.67072984111125 --cp-min 2 --n-ceil 0.194120055064654,1.20859537703479 --trim5 9 --cp-ival 1 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 681s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 681s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 681s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '2' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 681s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 681s Warning: skipping read '5' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 681s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '9' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 681s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '11' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 681s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 681s Warning: skipping read '15' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 681s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '25' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 681s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '27' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 681s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '36' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 681s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '38' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 681s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '40' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 681s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '42' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 681s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '43' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 681s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '49' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 681s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '50' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 681s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '56' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 681s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '59' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 681s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '61' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 681s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '62' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 681s 63 reads; of these: 681s 63 (100.00%) were unpaired; of these: 681s 55 (87.30%) aligned 0 times 681s 2 (3.17%) aligned exactly 1 time 681s 6 (9.52%) aligned >1 times 681s 12.70% overall alignment rate 681s Read 50 alignments... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GTGGT 681s GTGGT 681s Processing line... 681s GTGGT 681s GTGGT 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GGG 681s GGG 681s Processing line... 681s GGG 681s GGG 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s /usr/bin/bowtie2 --ma 34.3867470570251 --score-min L,2.99664466721695,3.73640098543562 -k 2 --rfg 24.3457038008537,6.67072984111125 --cp-min 2 --n-ceil 0.194120055064654,1.20859537703479 --trim5 9 --cp-ival 1 -f -p 4 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 681s GCTT 681s GCTT 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s AC 681s AC 681s Processing line... 681s AC 681s AC 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s AC 681s AC 681s Processing line... 681s AC 681s AC 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s TCCGGGTGG 681s TCCGGGTGG 681s Processing line... 681s TCCGGGTGG 681s TCCGGGTGG 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GC 681s GC 681s Processing line... 681s GC 681s GC 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GGGAAGACCGCGGCTCGGTCTGCGCC 681s GGGAAGACCGCGGCTCGGTCTGCGCC 681s --- Summary --- 681s Read 1 reference strings 681s Checked 14 alignments, 0 edits 681s --------------- 681s PASSED 681s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 681s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 681s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 681s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '2' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 681s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 681s Warning: skipping read '5' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 681s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '9' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 681s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '11' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 681s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 681s Warning: skipping read '15' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 681s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '25' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 681s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '27' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 681s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '36' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 681s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '38' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 681s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '40' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 681s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '42' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 681s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '43' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 681s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '49' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 681s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '50' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 681s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '56' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 681s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '59' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 681s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '61' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 681s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '62' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 681s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 681s 63 reads; of these: 681s 63 (100.00%) were unpaired; of these: 681s 55 (87.30%) aligned 0 times 681s 2 (3.17%) aligned exactly 1 time 681s 6 (9.52%) aligned >1 times 681s 12.70% overall alignment rate 681s Flattened IUPAC characters 681s Mutating sequence Sim.pm.2 681s Introducing 14 SNPs, 1/1 ref/read gaps, and 1 rearrangements 681s Finished SNPs 681s Finished ref gaps 681s Finished read gaps 681s Mutating sequence Sim.pm.1 681s Introducing 4 SNPs, 1/1 ref/read gaps, and 0 rearrangements 681s Finished SNPs 681s Finished ref gaps 681s Finished read gaps 681s Mutated reference genome to subject genome 681s SNPs introduced: 18 681s Reference gaps introduced: 2 681s Read gaps introduced: 2 681s Rearrangements introduced: 1 681s Created read sampler 681s Sampling 62 reads 681s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 681s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 681s parsing sequence Sim.pm.1... 681s parsing sequence Sim.pm.2... 681s Parsed 143 reference bases 681s *** Run 83 of 100 681s /usr/bin/bowtie2 --cp-min 5 --rdg 25.7413929719564,10.9375488104726 --score-min L,8.67162524167828,1.6251964048211 --ma 33.9481042435341 --cp-ival 1 -a --norc --trim5 2 --rfg 8.78278549459612 --mp 4.99345170866856,2.10825583022169 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 681s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 681s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 681s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '4' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 681s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '6' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 681s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '7' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 681s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '17' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 681s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '23' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 681s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '25' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 681s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '33' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 681s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 681s Warning: skipping read '35' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 681s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '42' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 681s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 681s Warning: skipping read '47' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 681s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 681s Warning: skipping read '58' because it was < 2 characters long 681s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 681s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 681s 62 reads; of these: 681s 62 (100.00%) were unpaired; of these: 681s 53 (85.48%) aligned 0 times 681s 7 (11.29%) aligned exactly 1 time 681s 2 (3.23%) aligned >1 times 681s 14.52% overall alignment rate 681s Read 50 alignments... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s AA 681s AA 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s AGGC 681s AGGC 681s Processing line... 681s AGGC 681s AGGC 681s Processing line... 681s AGGC 681s AGGC 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GCGGGAAGAC 681s GCGGGAAGAC 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GGTGGTGTTGAGAGGGTGACAGAG 681s GGTGGTGTTGAGAGGGTGACAGAG 681s Processing line... 681s Processing line... 681s Processing line... 681s GAGAGGG 681s GAGAGGG 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GTG 681s GTG 681s Processing line... 681s GTG 681s GTG 681s Processing line... 681s GTG 681s GTG 681s Processing line... 681s GTG 681s GTG 681s Processing line... 681s GTG 681s GTG 681s Processing line... 681s GTG 681s GTG 681s Processing line... 681s GTG 681s GTG 681s Processing line... 681s GTG 681s GTG 681s Processing line... 681s GTG 681s GTG 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s AGGGGGGGACTGG 681s AGGGGGGGACTGG 681s Processing line... 681s GGCGGT 681s GGCGGT 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GCGGGAAGAC 681s GCGGGAAGAC 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s --- Summary --- 681s Read 1 reference strings 681s Checked 19 alignments, 0 edits 681s --------------- 681s PASSED 681s Flattened IUPAC characters 681s Mutating sequence Sim.pm.1 681s Introducing 3 SNPs, 2/4 ref/read gaps, and 2 rearrangements 681s Finished SNPs 681s Finished ref gaps 681s Finished read gaps 681s Mutating sequence Sim.pm.2 681s Introducing 11 SNPs, 0/2 ref/read gaps, and 0 rearrangements 681s Finished SNPs 681s Finished ref gaps 681s Finished read gaps 681s Mutated reference genome to subject genome 681s SNPs introduced: 14 681s Reference gaps introduced: 2 681s Read gaps introduced: 6 681s Rearrangements introduced: 2 681s Created read sampler 681s Sampling 75 reads 681s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 681s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 681s *** Run 84 of 100 681s /usr/bin/bowtie2 --cp-ival 1 --local --trim5 7 --cp-min 2 -i C,0.832372000790956 --mp 1.87564808383122,1.10884431435343 --trim3 1 --score-min L,7.9986802380941,4.78971459908678 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 681s parsing sequence Sim.pm.1... 681s parsing sequence Sim.pm.2... 681s Parsed 143 reference bases 681s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #2 of read '10' because it was < 2 characters long 681s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '13' because it was < 2 characters long 681s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '14' because it was < 2 characters long 681s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '17' because it was < 2 characters long 681s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '36' because it was < 2 characters long 681s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '40' because it was < 2 characters long 681s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '43' because it was < 2 characters long 681s Warning: skipping mate #2 of read '43' because it was < 2 characters long 681s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '48' because it was < 2 characters long 681s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '50' because it was < 2 characters long 681s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '51' because it was < 2 characters long 681s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '56' because it was < 2 characters long 681s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 681s Warning: skipping read '60' because it was < 2 characters long 681s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '61' because it was < 2 characters long 681s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '63' because it was < 2 characters long 681s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #2 of read '65' because it was < 2 characters long 681s Read 50 alignments... 681s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '67' because it was < 2 characters long 681s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '69' because it was < 2 characters long 681s Read 100 alignments... 681s 75 reads; of these: 681s 58 (77.33%) were paired; of these: 681s 58 (100.00%) aligned concordantly 0 times 681s 0 (0.00%) aligned concordantly exactly 1 time 681s 0 (0.00%) aligned concordantly >1 times 681s ---- 681s 58 pairs aligned concordantly 0 times; of these: 681s 0 (0.00%) aligned discordantly 1 time 681s ---- 681s 58 pairs aligned 0 times concordantly or discordantly; of these: 681s 116 mates make up the pairs; of these: 681s 116 (100.00%) aligned 0 times 681s 0 (0.00%) aligned exactly 1 time 681s 0 (0.00%) aligned >1 times 681s 17 (22.67%) were unpaired; of these: 681s 17 (100.00%) aligned 0 times 681s 0 (0.00%) aligned exactly 1 time 681s 0 (0.00%) aligned >1 times 681s 0.00% overall alignment rate 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s /usr/bin/bowtie2 --cp-ival 1 --local --trim5 7 --cp-min 2 -i C,0.832372000790956 --mp 1.87564808383122,1.10884431435343 --trim3 1 --score-min L,7.9986802380941,4.78971459908678 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s --- Summary --- 681s Read 1 reference strings 681s Checked 0 alignments, 0 edits 681s --------------- 681s PASSED 681s ALSO checking that bowtie2 and bowtie2-align match up 681s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #2 of read '10' because it was < 2 characters long 681s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '13' because it was < 2 characters long 681s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '14' because it was < 2 characters long 681s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '17' because it was < 2 characters long 681s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '36' because it was < 2 characters long 681s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '40' because it was < 2 characters long 681s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '43' because it was < 2 characters long 681s Warning: skipping mate #2 of read '43' because it was < 2 characters long 681s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '48' because it was < 2 characters long 681s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '50' because it was < 2 characters long 681s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '51' because it was < 2 characters long 681s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '56' because it was < 2 characters long 681s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 681s Warning: skipping read '60' because it was < 2 characters long 681s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '61' because it was < 2 characters long 681s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '63' because it was < 2 characters long 681s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #2 of read '65' because it was < 2 characters long 681s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '67' because it was < 2 characters long 681s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '69' because it was < 2 characters long 681s 75 reads; of these: 681s 58 (77.33%) were paired; of these: 681s 58 (100.00%) aligned concordantly 0 times 681s 0 (0.00%) aligned concordantly exactly 1 time 681s 0 (0.00%) aligned concordantly >1 times 681s ---- 681s 58 pairs aligned concordantly 0 times; of these: 681s 0 (0.00%) aligned discordantly 1 time 681s ---- 681s 58 pairs aligned 0 times concordantly or discordantly; of these: 681s 116 mates make up the pairs; of these: 681s 116 (100.00%) aligned 0 times 681s 0 (0.00%) aligned exactly 1 time 681s 0 (0.00%) aligned >1 times 681s 17 (22.67%) were unpaired; of these: 681s 17 (100.00%) aligned 0 times 681s 0 (0.00%) aligned exactly 1 time 681s 0 (0.00%) aligned >1 times 681s 0.00% overall alignment rate 681s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 681s /usr/bin/bowtie2 --cp-ival 1 --local --trim5 7 --cp-min 2 -i C,0.832372000790956 --mp 1.87564808383122,1.10884431435343 --trim3 1 --score-min L,7.9986802380941,4.78971459908678 -q -p 3 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 681s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 681s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #2 of read '10' because it was < 2 characters long 681s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '13' because it was < 2 characters long 681s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '14' because it was < 2 characters long 681s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '17' because it was < 2 characters long 681s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '36' because it was < 2 characters long 681s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '40' because it was < 2 characters long 681s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '43' because it was < 2 characters long 681s Warning: skipping mate #2 of read '43' because it was < 2 characters long 681s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 681s Warning: skipping read '48' because it was < 2 characters long 681s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '50' because it was < 2 characters long 681s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '51' because it was < 2 characters long 681s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '56' because it was < 2 characters long 681s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 681s Warning: skipping read '60' because it was < 2 characters long 681s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '61' because it was < 2 characters long 681s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '63' because it was < 2 characters long 681s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #2 of read '65' because it was < 2 characters long 681s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '67' because it was < 2 characters long 681s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '69' because it was < 2 characters long 681s 75 reads; of these: 681s 58 (77.33%) were paired; of these: 681s 58 (100.00%) aligned concordantly 0 times 681s 0 (0.00%) aligned concordantly exactly 1 time 681s 0 (0.00%) aligned concordantly >1 times 681s ---- 681s 58 pairs aligned concordantly 0 times; of these: 681s 0 (0.00%) aligned discordantly 1 time 681s ---- 681s 58 pairs aligned 0 times concordantly or discordantly; of these: 681s 116 mates make up the pairs; of these: 681s 116 (100.00%) aligned 0 times 681s 0 (0.00%) aligned exactly 1 time 681s 0 (0.00%) aligned >1 times 681s 17 (22.67%) were unpaired; of these: 681s 17 (100.00%) aligned 0 times 681s 0 (0.00%) aligned exactly 1 time 681s 0 (0.00%) aligned >1 times 681s 0.00% overall alignment rate 681s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 681s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 681s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 681s *** Run 85 of 100 681s /usr/bin/bowtie2 --trim3 1 --score-min L,4.27474662072652,1.39178118775664 -N 0 -L20 --local --cp-ival 1 --cp-min 6 --norc -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw 681s Flattened IUPAC characters 681s Mutating sequence Sim.pm.2 681s Introducing 11 SNPs, 1/1 ref/read gaps, and 0 rearrangements 681s Finished SNPs 681s Finished ref gaps 681s Finished read gaps 681s Mutating sequence Sim.pm.1 681s Introducing 13 SNPs, 0/1 ref/read gaps, and 0 rearrangements 681s Finished SNPs 681s Finished ref gaps 681s Finished read gaps 681s Mutated reference genome to subject genome 681s SNPs introduced: 24 681s Reference gaps introduced: 1 681s Read gaps introduced: 2 681s Rearrangements introduced: 0 681s Created read sampler 681s Sampling 51 reads 681s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 681s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 681s parsing sequence Sim.pm.1... 681s parsing sequence Sim.pm.2... 681s Parsed 143 reference bases 681s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 681s Warning: skipping read '16' because it was < 2 characters long 681s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 681s Warning: skipping read '41' because it was < 2 characters long 681s 51 reads; of these: 681s 51 (100.00%) were unpaired; of these: 681s 45 (88.24%) aligned 0 times 681s 6 (11.76%) aligned exactly 1 time 681s 0 (0.00%) aligned >1 times 681s 11.76% overall alignment rate 681s Read 50 alignments... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GGTGGTAGGGGGGGACT 681s GGTGGTAGGGGGGGACT 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GGCTCGG 681s GGCTCGG 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GGACTGGCGGGAAGACCGCGGCT 681s GGACTGGCGGGAAGACCGCGGCT 681s Processing line... 681s GGCTCGG 681s GGCTCGG 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GAGCTGG 681s GAGCTGG 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s GGGGGGGACTGGCGGGAAGACCGCGGCT 681s GGGGGGGACTGGCGGGAAGACCGCGGCT 681s Processing line... 681s Processing line... 681s --- Summary --- 681s Read 1 reference strings 681s Checked 6 alignments, 0 edits 681s --------------- 681s PASSED 681s Flattened IUPAC characters 681s Mutating sequence Sim.pm.2 681s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 681s Finished SNPs 681s Finished ref gaps 681s Finished read gaps 681s Mutating sequence Sim.pm.1 681s Introducing 14 SNPs, 1/1 ref/read gaps, and 1 rearrangements 681s Finished SNPs 681s Finished ref gaps 681s Finished read gaps 681s Mutated reference genome to subject genome 681s SNPs introduced: 21 681s Reference gaps introduced: 2 681s Read gaps introduced: 1 681s Rearrangements introduced: 1 681s Created read sampler 681s Sampling 38 reads 681s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 681s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 681s parsing sequence Sim.pm.1... 681s *** Run 86 of 100 681s /usr/bin/bowtie2 --trim5 5 --local --cp-ival 1 --nofw --cp-min 2 --np 5 --score-min L,2.33194643408779,6.90648830917268 -D 44 --mm -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta 681s parsing sequence Sim.pm.2... 681s Parsed 143 reference bases 681s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '1' because it was < 2 characters long 681s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '2' because it was < 2 characters long 681s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '14' because it was < 2 characters long 681s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '17' because it was < 2 characters long 681s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '31' because it was < 2 characters long 681s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #2 of read '37' because it was < 2 characters long 681s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '38' because it was < 2 characters long 681s 38 reads; of these: 681s 37 (97.37%) were paired; of these: 681s 37 (100.00%) aligned concordantly 0 times 681s 0 (0.00%) aligned concordantly exactly 1 time 681s 0 (0.00%) aligned concordantly >1 times 681s ---- 681s 37 pairs aligned concordantly 0 times; of these: 681s 0 (0.00%) aligned discordantly 1 time 681s ---- 681s 37 pairs aligned 0 times concordantly or discordantly; of these: 681s 74 mates make up the pairs; of these: 681s 74 (100.00%) aligned 0 times 681s 0 (0.00%) aligned exactly 1 time 681s 0 (0.00%) aligned >1 times 681s 1 (2.63%) were unpaired; of these: 681s 1 (100.00%) aligned 0 times 681s 0 (0.00%) aligned exactly 1 time 681s 0 (0.00%) aligned >1 times 681s 0.00% overall alignment rate 681s Read 50 alignments... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s Processing line... 681s --- Summary --- 681s Read 1 reference strings 681s Checked 0 alignments, 0 edits 681s --------------- 681s PASSED 681s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 681s /usr/bin/bowtie2 --trim5 5 --local --cp-ival 1 --nofw --cp-min 2 --np 5 --score-min L,2.33194643408779,6.90648830917268 -D 44 --mm -f -p 2 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 681s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '1' because it was < 2 characters long 681s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '2' because it was < 2 characters long 681s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '14' because it was < 2 characters long 681s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '17' because it was < 2 characters long 681s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '31' because it was < 2 characters long 681s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 681s Warning: skipping mate #2 of read '37' because it was < 2 characters long 681s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 681s Warning: skipping mate #1 of read '38' because it was < 2 characters long 682s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 682s 38 reads; of these: 682s 37 (97.37%) were paired; of these: 682s 37 (100.00%) aligned concordantly 0 times 682s 0 (0.00%) aligned concordantly exactly 1 time 682s 0 (0.00%) aligned concordantly >1 times 682s ---- 682s 37 pairs aligned concordantly 0 times; of these: 682s 0 (0.00%) aligned discordantly 1 time 682s ---- 682s 37 pairs aligned 0 times concordantly or discordantly; of these: 682s 74 mates make up the pairs; of these: 682s 74 (100.00%) aligned 0 times 682s 0 (0.00%) aligned exactly 1 time 682s 0 (0.00%) aligned >1 times 682s 1 (2.63%) were unpaired; of these: 682s 1 (100.00%) aligned 0 times 682s 0 (0.00%) aligned exactly 1 time 682s 0 (0.00%) aligned >1 times 682s 0.00% overall alignment rate 682s Flattened IUPAC characters 682s Mutating sequence Sim.pm.2 682s Introducing 9 SNPs, 0/0 ref/read gaps, and 1 rearrangements 682s Finished SNPs 682s Finished ref gaps 682s Finished read gaps 682s Mutating sequence Sim.pm.1 682s Introducing 19 SNPs, 2/0 ref/read gaps, and 1 rearrangements 682s Finished SNPs 682s Finished ref gaps 682s Finished read gaps 682s Mutated reference genome to subject genome 682s SNPs introduced: 28 682s Reference gaps introduced: 2 682s Read gaps introduced: 0 682s Rearrangements introduced: 2 682s Created read sampler 682s Sampling 72 reads 682s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 682s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 682s parsing sequence Sim.pm.1... 682s parsing sequence Sim.pm.2... 682s Parsed 143 reference bases 682s *** Run 87 of 100 682s /usr/bin/bowtie2 --score-min L,2.26950361249401,4.87266594366012 -R 4 --mp 8.67731077902551,4.59875289345812 -D 49 -k 2 --mm --cp-min 7 --norc --cp-ival 2 -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw 682s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 682s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 682s Warning: skipping read '35' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 682s 72 reads; of these: 682s 72 (100.00%) were unpaired; of these: 682s 60 (83.33%) aligned 0 times 682s 5 (6.94%) aligned exactly 1 time 682s 7 (9.72%) aligned >1 times 682s 16.67% overall alignment rate 682s Read 50 alignments... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s TC 682s TC 682s Processing line... 682s TC 682s TC 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s GA 682s GA 682s Processing line... 682s GA 682s GA 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s TGGCGGGAAGAC 682s TGGCGGGAAGAC 682s Processing line... 682s Processing line... 682s CAGAGGC 682s CAGAGGC 682s Processing line... 682s CGTG 682s CGTG 682s Processing line... 682s CGTG 682s CGTG 682s Processing line... 682s GA 682s GA 682s Processing line... 682s GA 682s GA 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s TGTTG 682s TGTTG 682s Processing line... 682s TGTTG 682s TGTTG 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s GGGGGGGACTGGCGGGAAGACCGC 682s GGGGGGGACTGGCGGGAAGACCGC 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s CGCGGCTCGGT 682s CGCGGCTCGGT 682s Processing line... 682s GCTTAGGCGGTC 682s GCTTAGGCGGTC 682s Processing line... 682s Processing line... 682s Processing line... 682s TGT 682s TGT 682s Processing line... 682s TGT 682s TGT 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s GGC 682s GGC 682s Processing line... 682s GGC 682s GGC 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s --- Summary --- 682s Read 1 reference strings 682s Checked 19 alignments, 0 edits 682s --------------- 682s PASSED 682s Flattened IUPAC characters 682s Mutating sequence Sim.pm.2 682s Introducing 0 SNPs, 0/1 ref/read gaps, and 2 rearrangements 682s Finished SNPs 682s Finished ref gaps 682s Finished read gaps 682s Mutating sequence Sim.pm.1 682s Introducing 19 SNPs, 0/0 ref/read gaps, and 0 rearrangements 682s Finished SNPs 682s Finished ref gaps 682s Finished read gaps 682s Mutated reference genome to subject genome 682s SNPs introduced: 19 682s Reference gaps introduced: 0 682s Read gaps introduced: 1 682s Rearrangements introduced: 2 682s Created read sampler 682s Sampling 86 reads 682s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 682s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 682s parsing sequence Sim.pm.1... 682s parsing sequence Sim.pm.2... 682s Parsed 143 reference bases 682s *** Run 88 of 100 682s /usr/bin/bowtie2 --rfg 15.7326848382494 --mp 5.98975400772369,2.52801101742356 -i S,0.435541632129363,2.23756630820834 --local --cp-ival 1 -a --trim5 6 --norc --score-min L,7.35082243514243,4.52863256257669 --cp-min 2 --np 4 -q -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq 682s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 682s Warning: skipping read '1' because it was < 2 characters long 682s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '4' because it was < 2 characters long 682s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '23' because it was < 2 characters long 682s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '40' because it was < 2 characters long 682s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '46' because it was < 2 characters long 682s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '52' because it was < 2 characters long 682s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '53' because it was < 2 characters long 682s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '55' because it was < 2 characters long 682s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '56' because it was < 2 characters long 682s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '70' because it was < 2 characters long 682s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '77' because it was < 2 characters long 682s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '79' because it was < 2 characters long 682s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '85' because it was < 2 characters long 682s 86 reads; of these: 682s 86 (100.00%) were unpaired; of these: 682s 86 (100.00%) aligned 0 times 682s 0 (0.00%) aligned exactly 1 time 682s 0 (0.00%) aligned >1 times 682s 0.00% overall alignment rate 682s Read 50 alignments... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s --- Summary --- 682s Read 1 reference strings 682s Checked 0 alignments, 0 edits 682s --------------- 682s PASSED 682s Flattened IUPAC characters 682s Mutating sequence Sim.pm.1 682s Introducing 14 SNPs, 0/1 ref/read gaps, and 1 rearrangements 682s Finished SNPs 682s Finished ref gaps 682s Finished read gaps 682s Mutating sequence Sim.pm.2 682s Introducing 5 SNPs, 2/0 ref/read gaps, and 1 rearrangements 682s Finished SNPs 682s Finished ref gaps 682s Finished read gaps 682s Mutated reference genome to subject genome 682s SNPs introduced: 19 682s Reference gaps introduced: 2 682s Read gaps introduced: 1 682s Rearrangements introduced: 2 682s Created read sampler 682s Sampling 62 reads 682s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 682s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 682s parsing sequence Sim.pm.1... 682s parsing sequence Sim.pm.2... 682s Parsed 143 reference bases 682s *** Run 89 of 100 682s /usr/bin/bowtie2 -k 6 -D 11 -N 1 -L15 --score-min L,7.66449395077396,7.79498404477427 --nofw --trim3 6 --cp-ival 3 --cp-min 2 --np 8 -q -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq 682s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 682s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '6' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 682s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '7' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 682s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '15' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 682s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '18' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 682s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '25' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 682s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '29' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 682s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '30' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 682s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '41' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 682s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '46' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 682s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '53' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 682s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '57' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 682s Warning: skipping read '62' because length (1) <= # seed mismatches (1) 682s Warning: skipping read '62' because it was < 2 characters long 682s 62 reads; of these: 682s 62 (100.00%) were unpaired; of these: 682s 54 (87.10%) aligned 0 times 682s 4 (6.45%) aligned exactly 1 time 682s 4 (6.45%) aligned >1 times 682s 12.90% overall alignment rate 682s Read 50 alignments... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s GG 682s GG 682s Processing line... 682s GG 682s GG 682s Processing line... 682s GG 682s GG 682s Processing line... 682s GG 682s GG 682s Processing line... 682s GG 682s GG 682s Processing line... 682s GG 682s GG 682s Processing line... 682s TAGGGGGGGACTGGCGGGAAGACCGCGG 682s TAGGGGGGGACTGGCGGGAAGACCGCGG 682s Processing line... 682s GTGGTAGGGGGGGACTGGCGGG 682s GTGGTAGGGGGGGACTGGCGGG 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s GAGGGT 682s GAGGGT 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s TCC 682s TCC 682s Processing line... 682s TCC 682s TCC 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s ACTGGCGGGAAGA 682s ACTGGCGGGAAGA 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s /usr/bin/bowtie2 -k 6 -D 11 -N 1 -L15 --score-min L,7.66449395077396,7.79498404477427 --nofw --trim3 6 --cp-ival 3 --cp-min 2 --np 8 -q -p 2 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 682s CGGGTG 682s CGGGTG 682s Processing line... 682s CGGGTG 682s CGGGTG 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s --- Summary --- 682s Read 1 reference strings 682s Checked 20 alignments, 0 edits 682s --------------- 682s PASSED 682s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 682s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 682s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '6' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 682s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '7' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 682s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '15' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 682s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '18' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 682s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '25' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 682s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '29' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 682s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '30' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 682s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '41' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 682s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '46' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 682s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '53' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 682s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '57' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 682s Warning: skipping read '62' because length (1) <= # seed mismatches (1) 682s Warning: skipping read '62' because it was < 2 characters long 682s 62 reads; of these: 682s 62 (100.00%) were unpaired; of these: 682s 54 (87.10%) aligned 0 times 682s 4 (6.45%) aligned exactly 1 time 682s 4 (6.45%) aligned >1 times 682s 12.90% overall alignment rate 682s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 682s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 682s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 682s Flattened IUPAC characters 682s Mutating sequence Sim.pm.1 682s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 682s Finished SNPs 682s Finished ref gaps 682s Finished read gaps 682s Mutating sequence Sim.pm.2 682s Introducing 10 SNPs, 0/1 ref/read gaps, and 0 rearrangements 682s Finished SNPs 682s Finished ref gaps 682s Finished read gaps 682s Mutated reference genome to subject genome 682s SNPs introduced: 19 682s Reference gaps introduced: 0 682s Read gaps introduced: 1 682s Rearrangements introduced: 0 682s Created read sampler 682s Sampling 56 reads 682s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 682s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 682s parsing sequence Sim.pm.1... 682s parsing sequence Sim.pm.2... 682s Parsed 143 reference bases 682s *** Run 90 of 100 682s /usr/bin/bowtie2 --gbar 2 --score-min L,3.94304340107305,2.45134465879029 --ma 38.8403764201477 --trim3 8 --mm --cp-min 2 --np 2 --cp-ival 2 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 682s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 682s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 682s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '1' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 682s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '2' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 682s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '3' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 682s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '10' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 682s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '12' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 682s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '15' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 682s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '16' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 682s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '23' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 682s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '34' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 682s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '35' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 682s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '42' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 682s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '48' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 682s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '49' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 682s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '53' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 682s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '54' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 682s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '56' because it was < 2 characters long 682s 56 reads; of these: 682s 56 (100.00%) were unpaired; of these: 682s 49 (87.50%) aligned 0 times 682s 1 (1.79%) aligned exactly 1 time 682s 6 (10.71%) aligned >1 times 682s 12.50% overall alignment rate 682s Read 50 alignments... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s TGG 682s TGG 682s /usr/bin/bowtie2 --gbar 2 --score-min L,3.94304340107305,2.45134465879029 --ma 38.8403764201477 --trim3 8 --mm --cp-min 2 --np 2 --cp-ival 2 -f -p 3 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s AGGCGTGG 682s AGGCGTGG 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s AGCTTAGGCGGTC 682s AGCTTAGGCGGTC 682s Processing line... 682s Processing line... 682s Processing line... 682s CCAGC 682s CCAGC 682s Processing line... 682s TGG 682s TGG 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s TCCGGG 682s TCCGGG 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s TCCGGGTGGTG 682s TCCGGGTGGTG 682s Processing line... 682s --- Summary --- 682s Read 1 reference strings 682s Checked 7 alignments, 0 edits 682s --------------- 682s PASSED 682s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 682s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 682s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 682s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '1' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 682s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '2' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 682s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '3' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 682s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '10' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 682s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '12' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 682s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '15' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 682s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '16' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 682s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '23' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 682s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '34' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 682s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '35' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 682s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '42' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 682s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '48' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 682s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '49' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 682s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '53' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 682s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '54' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 682s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '56' because it was < 2 characters long 682s 56 reads; of these: 682s 56 (100.00%) were unpaired; of these: 682s 49 (87.50%) aligned 0 times 682s 1 (1.79%) aligned exactly 1 time 682s 6 (10.71%) aligned >1 times 682s 12.50% overall alignment rate 682s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 682s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 682s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 682s *** Run 91 of 100 682s /usr/bin/bowtie2 --score-min L,4.15611299745254,2.74936447837203 -D 24 --gbar 6 --mm --cp-min 2 --trim3 6 --nofw -N 1 -L20 --mp 7.77317448692389,4.14919948609637 --rfg 5.72847869243505,13.0249377796984 -a --cp-ival 2 -f -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.fasta 682s Flattened IUPAC characters 682s Mutating sequence Sim.pm.1 682s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 682s Finished SNPs 682s Finished ref gaps 682s Finished read gaps 682s Mutating sequence Sim.pm.2 682s Introducing 5 SNPs, 1/1 ref/read gaps, and 0 rearrangements 682s Finished SNPs 682s Finished ref gaps 682s Finished read gaps 682s Mutated reference genome to subject genome 682s SNPs introduced: 7 682s Reference gaps introduced: 1 682s Read gaps introduced: 1 682s Rearrangements introduced: 1 682s Created read sampler 682s Sampling 53 reads 682s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 682s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 682s parsing sequence Sim.pm.1... 682s parsing sequence Sim.pm.2... 682s Parsed 143 reference bases 682s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 682s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '10' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 682s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '21' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 682s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '22' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 682s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '24' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 682s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '40' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 682s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '43' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 682s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '48' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 682s /usr/bin/bowtie2 --score-min L,4.15611299745254,2.74936447837203 -D 24 --gbar 6 --mm --cp-min 2 --trim3 6 --nofw -N 1 -L20 --mp 7.77317448692389,4.14919948609637 --rfg 5.72847869243505,13.0249377796984 -a --cp-ival 2 -f -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder /tmp/Sim.pm.HBgkkIzX_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 682s 53 reads; of these: 682s 53 (100.00%) were unpaired; of these: 682s 44 (83.02%) aligned 0 times 682s 4 (7.55%) aligned exactly 1 time 682s 5 (9.43%) aligned >1 times 682s 16.98% overall alignment rate 682s Read 50 alignments... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s CC 682s CC 682s Processing line... 682s CC 682s CC 682s Processing line... 682s CC 682s CC 682s Processing line... 682s CC 682s CC 682s Processing line... 682s CC 682s CC 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s AGACCGCGGCTCGGTCT 682s AGACCGCGGCTCGGTCT 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s AGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGT 682s AGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGT 682s Processing line... 682s GGTGACA 682s GGTGACA 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s TAGGGGGGGACTGGCG 682s TAGGGGGGGACTGGCG 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s CGG 682s CGG 682s Processing line... 682s CGG 682s CGG 682s Processing line... 682s CGG 682s CGG 682s Processing line... 682s CGG 682s CGG 682s Processing line... 682s CGG 682s CGG 682s Processing line... 682s CGG 682s CGG 682s Processing line... 682s Processing line... 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s CG 682s CG 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s TC 682s TC 682s Processing line... 682s TC 682s TC 682s Processing line... 682s TC 682s TC 682s Processing line... 682s TC 682s TC 682s Processing line... 682s TC 682s TC 682s Processing line... 682s CC 682s CC 682s Processing line... 682s CC 682s CC 682s Processing line... 682s CC 682s CC 682s Processing line... 682s CC 682s CC 682s Processing line... 682s CC 682s CC 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s --- Summary --- 682s Read 1 reference strings 682s Checked 35 alignments, 0 edits 682s --------------- 682s PASSED 682s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 682s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 682s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '10' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 682s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '21' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 682s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '22' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 682s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '24' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 682s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '40' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 682s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '43' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 682s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 682s Warning: skipping read '48' because it was < 2 characters long 682s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 682s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 682s 53 reads; of these: 682s 53 (100.00%) were unpaired; of these: 682s 44 (83.02%) aligned 0 times 682s 4 (7.55%) aligned exactly 1 time 682s 5 (9.43%) aligned >1 times 682s 16.98% overall alignment rate 682s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 682s Flattened IUPAC characters 682s *** Run 92 of 100 682s /usr/bin/bowtie2 --trim3 4 --rfg 30.6704069827612 --n-ceil 0.892147263666856,1.17484383627853 --trim5 9 -M 3 --cp-ival 4 --local -R 2 --score-min L,1.29533880907288,6.4020005642297 --mm --rdg 28.7140699865743,8.12128386241809 --cp-min 2 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 682s Mutating sequence Sim.pm.1 682s Introducing 0 SNPs, 1/3 ref/read gaps, and 0 rearrangements 682s Finished SNPs 682s Finished ref gaps 682s Finished read gaps 682s Mutating sequence Sim.pm.2 682s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 682s Finished SNPs 682s Finished ref gaps 682s Finished read gaps 682s Mutated reference genome to subject genome 682s SNPs introduced: 7 682s Reference gaps introduced: 2 682s Read gaps introduced: 3 682s Rearrangements introduced: 0 682s Created read sampler 682s Sampling 61 reads 682s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 682s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 682s parsing sequence Sim.pm.1... 682s parsing sequence Sim.pm.2... 682s Parsed 143 reference bases 682s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 682s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '1' because it was < 2 characters long 682s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '3' because it was < 2 characters long 682s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '5' because it was < 2 characters long 682s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '6' because it was < 2 characters long 682s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '7' because it was < 2 characters long 682s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '8' because it was < 2 characters long 682s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '9' because it was < 2 characters long 682s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '10' because it was < 2 characters long 682s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '18' because it was < 2 characters long 682s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '23' because it was < 2 characters long 682s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '45' because it was < 2 characters long 682s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '46' because it was < 2 characters long 682s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '52' because it was < 2 characters long 682s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '55' because it was < 2 characters long 682s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '61' because it was < 2 characters long 682s 61 reads; of these: 682s 43 (70.49%) were paired; of these: 682s 43 (100.00%) aligned concordantly 0 times 682s 0 (0.00%) aligned concordantly exactly 1 time 682s 0 (0.00%) aligned concordantly >1 times 682s ---- 682s 43 pairs aligned concordantly 0 times; of these: 682s 0 (0.00%) aligned discordantly 1 time 682s ---- 682s 43 pairs aligned 0 times concordantly or discordantly; of these: 682s 86 mates make up the pairs; of these: 682s 86 (100.00%) aligned 0 times 682s 0 (0.00%) aligned exactly 1 time 682s 0 (0.00%) aligned >1 times 682s 18 (29.51%) were unpaired; of these: 682s 18 (100.00%) aligned 0 times 682s 0 (0.00%) aligned exactly 1 time 682s 0 (0.00%) aligned >1 times 682s 0.00% overall alignment rate 682s Read 50 alignments... 682s Read 100 alignments... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s /usr/bin/bowtie2 --trim3 4 --rfg 30.6704069827612 --n-ceil 0.892147263666856,1.17484383627853 --trim5 9 -M 3 --cp-ival 4 --local -R 2 --score-min L,1.29533880907288,6.4020005642297 --mm --rdg 28.7140699865743,8.12128386241809 --cp-min 2 -q -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s Processing line... 682s --- Summary --- 682s Read 1 reference strings 682s Checked 0 alignments, 0 edits 682s --------------- 682s PASSED 682s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 682s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 682s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '1' because it was < 2 characters long 682s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '3' because it was < 2 characters long 682s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '5' because it was < 2 characters long 682s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '6' because it was < 2 characters long 682s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '7' because it was < 2 characters long 682s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '8' because it was < 2 characters long 682s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '9' because it was < 2 characters long 682s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '10' because it was < 2 characters long 682s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '18' because it was < 2 characters long 682s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '23' because it was < 2 characters long 682s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 682s Warning: skipping read '45' because it was < 2 characters long 682s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '46' because it was < 2 characters long 682s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '52' because it was < 2 characters long 682s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '55' because it was < 2 characters long 682s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 682s Warning: skipping mate #1 of read '61' because it was < 2 characters long 682s 61 reads; of these: 682s 43 (70.49%) were paired; of these: 682s 43 (100.00%) aligned concordantly 0 times 682s 0 (0.00%) aligned concordantly exactly 1 time 682s 0 (0.00%) aligned concordantly >1 times 682s ---- 682s 43 pairs aligned concordantly 0 times; of these: 682s 0 (0.00%) aligned discordantly 1 time 682s ---- 682s 43 pairs aligned 0 times concordantly or discordantly; of these: 682s 86 mates make up the pairs; of these: 682s 86 (100.00%) aligned 0 times 682s 0 (0.00%) aligned exactly 1 time 682s 0 (0.00%) aligned >1 times 682s 18 (29.51%) were unpaired; of these: 682s 18 (100.00%) aligned 0 times 682s 0 (0.00%) aligned exactly 1 time 682s 0 (0.00%) aligned >1 times 682s 0.00% overall alignment rate 682s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 683s *** Run 93 of 100 683s /usr/bin/bowtie2 --cp-ival 1 --norc --trim5 1 --cp-min 2 --rfg 28.0111535484661,14.0555262648127 -k 3 --score-min L,2.96369369044619,4.38403743907957 --ma 19.3008964860701 --trim3 2 -f -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta 683s Flattened IUPAC characters 683s Mutating sequence Sim.pm.2 683s Introducing 4 SNPs, 0/1 ref/read gaps, and 1 rearrangements 683s Finished SNPs 683s Finished ref gaps 683s Finished read gaps 683s Mutating sequence Sim.pm.1 683s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 683s Finished SNPs 683s Finished ref gaps 683s Finished read gaps 683s Mutated reference genome to subject genome 683s SNPs introduced: 4 683s Reference gaps introduced: 0 683s Read gaps introduced: 1 683s Rearrangements introduced: 2 683s Created read sampler 683s Sampling 84 reads 683s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fasta & /tmp/Sim.pm.HBgkkIzX_2.fasta 683s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 683s parsing sequence Sim.pm.1... 683s parsing sequence Sim.pm.2... 683s Parsed 143 reference bases 683s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 683s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '7' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 683s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '9' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 683s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '12' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 683s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '17' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 683s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '25' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 683s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '32' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 683s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '47' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 683s Read 50 alignments... 683s Read 100 alignments... 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 683s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '68' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 683s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '72' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 683s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '79' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 683s 84 reads; of these: 683s 75 (89.29%) were paired; of these: 683s 75 (100.00%) aligned concordantly 0 times 683s 0 (0.00%) aligned concordantly exactly 1 time 683s 0 (0.00%) aligned concordantly >1 times 683s ---- 683s 75 pairs aligned concordantly 0 times; of these: 683s 0 (0.00%) aligned discordantly 1 time 683s ---- 683s 75 pairs aligned 0 times concordantly or discordantly; of these: 683s 150 mates make up the pairs; of these: 683s 130 (86.67%) aligned 0 times 683s 13 (8.67%) aligned exactly 1 time 683s 7 (4.67%) aligned >1 times 683s 9 (10.71%) were unpaired; of these: 683s 6 (66.67%) aligned 0 times 683s 1 (11.11%) aligned exactly 1 time 683s 2 (22.22%) aligned >1 times 683s 14.47% overall alignment rate 683s Read 150 alignments... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s GAA 683s GAA 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s GG 683s GG 683s Processing line... 683s GG 683s GG 683s Processing line... 683s GG 683s GG 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s GTGGTA 683s GTGGTA 683s Processing line... 683s Processing line... 683s GCTCGGTCTGCGCCCAGCTT 683s GCTCGGTCTGCGCCCAGCTT 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s GCC 683s GCC 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s TGTTGAGAG 683s TGTTGAGAG 683s Processing line... 683s Processing line... 683s TGGCGGGAAGACCGCGGCTCGGT 683s TGGCGGGAAGACCGCGGCTCGGT 683s Processing line... 683s Processing line... 683s GGGTGGTGTTG 683s GGGTGGTGTTG 683s Processing line... 683s GGGTGGTGTTG 683s GGGTGGTGTTG 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s GGGGGG 683s GGGGGG 683s Processing line... 683s GGGGGG 683s GGGGGG 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s GGGGGACTGGCGGGAA 683s GGGGGACTGGCGGGAA 683s Processing line... 683s Processing line... 683s GTCAGGAGGG 683s GTCAGGAGGG 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s TGG 683s TGG 683s Processing line... 683s TGG 683s TGG 683s Processing line... 683s TGG 683s TGG 683s Processing line... 683s TCC 683s TCC 683s Processing line... 683s TCC 683s TCC 683s Processing line... 683s Processing line... 683s ACTGG 683s ACTGG 683s Processing line... 683s Processing line... 683s GC 683s GC 683s Processing line... 683s GC 683s GC 683s Processing line... 683s GC 683s GC 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s GTAGGGGGGGACTGGCGGGAAGACCGCG 683s GTAGGGGGGGACTGGCGGGAAGACCGCG 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s GGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGG 683s GGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGG 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s TGGTGT 683s TGGTGT 683s Processing line... 683s TGGTGT 683s TGGTGT 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s AGGGGGGGACTGGCGGGAAGACCGCGG 683s AGGGGGGGACTGGCGGGAAGACCGCGG 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s GGGA 683s GGGA 683s Processing line... 683s GGGA 683s GGGA 683s Processing line... 683s GGGA 683s GGGA 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s GTGGT 683s GTGGT 683s Processing line... 683s GTGGT 683s GTGGT 683s Processing line... 683s GTGGT 683s GTGGT 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s GCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGG 683s GCGGGAAGACCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGG 683s Processing line... 683s Processing line... 683s Processing line... 683s TCG 683s TCG 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s --- Summary --- 683s Read 1 reference strings 683s Checked 37 alignments, 0 edits 683s --------------- 683s PASSED 683s /usr/bin/bowtie2 --cp-ival 1 --norc --trim5 1 --cp-min 2 --rfg 28.0111535484661,14.0555262648127 -k 3 --score-min L,2.96369369044619,4.38403743907957 --ma 19.3008964860701 --trim3 2 -f -p 2 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 683s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 683s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 683s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '7' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 683s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '9' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 683s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '12' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 683s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '17' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 683s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '25' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 683s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '32' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 683s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '47' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 683s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '68' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 683s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '72' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 683s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '79' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 683s 84 reads; of these: 683s 75 (89.29%) were paired; of these: 683s 75 (100.00%) aligned concordantly 0 times 683s 0 (0.00%) aligned concordantly exactly 1 time 683s 0 (0.00%) aligned concordantly >1 times 683s ---- 683s 75 pairs aligned concordantly 0 times; of these: 683s 0 (0.00%) aligned discordantly 1 time 683s ---- 683s 75 pairs aligned 0 times concordantly or discordantly; of these: 683s 150 mates make up the pairs; of these: 683s 130 (86.67%) aligned 0 times 683s 13 (8.67%) aligned exactly 1 time 683s 7 (4.67%) aligned >1 times 683s 9 (10.71%) were unpaired; of these: 683s 6 (66.67%) aligned 0 times 683s 1 (11.11%) aligned exactly 1 time 683s 2 (22.22%) aligned >1 times 683s 14.47% overall alignment rate 683s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 683s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 683s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 683s /usr/bin/bowtie2 --cp-ival 1 --norc --trim5 1 --cp-min 2 --rfg 28.0111535484661,14.0555262648127 -k 3 --score-min L,2.96369369044619,4.38403743907957 --ma 19.3008964860701 --trim3 2 -f -p 2 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.fasta -2 /tmp/Sim.pm.HBgkkIzX_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 683s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 683s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 683s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '7' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 683s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '9' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 683s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '12' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 683s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '17' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 683s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '25' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 683s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '47' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 683s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '68' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 683s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '72' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 683s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '32' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 683s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '79' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 683s 84 reads; of these: 683s 75 (89.29%) were paired; of these: 683s 75 (100.00%) aligned concordantly 0 times 683s 0 (0.00%) aligned concordantly exactly 1 time 683s 0 (0.00%) aligned concordantly >1 times 683s ---- 683s 75 pairs aligned concordantly 0 times; of these: 683s 0 (0.00%) aligned discordantly 1 time 683s ---- 683s 75 pairs aligned 0 times concordantly or discordantly; of these: 683s 150 mates make up the pairs; of these: 683s 130 (86.67%) aligned 0 times 683s 13 (8.67%) aligned exactly 1 time 683s 7 (4.67%) aligned >1 times 683s 9 (10.71%) were unpaired; of these: 683s 6 (66.67%) aligned 0 times 683s 1 (11.11%) aligned exactly 1 time 683s 2 (22.22%) aligned >1 times 683s 14.47% overall alignment rate 683s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 683s *** Run 94 of 100 683s /usr/bin/bowtie2 --nofw --score-min L,8.94101429357483,6.36268297016064 -N 0 -L31 --gbar 5 --rdg 10.6966533922663 --mm --rfg 14.2343705822348 --cp-min 5 -M 2 --n-ceil 1.12026977665859,0.754910254928922 --trim5 1 --cp-ival 1 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 683s Flattened IUPAC characters 683s Mutating sequence Sim.pm.1 683s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 683s Finished SNPs 683s Finished ref gaps 683s Finished read gaps 683s Mutating sequence Sim.pm.2 683s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 683s Finished SNPs 683s Finished ref gaps 683s Finished read gaps 683s Mutated reference genome to subject genome 683s SNPs introduced: 12 683s Reference gaps introduced: 1 683s Read gaps introduced: 0 683s Rearrangements introduced: 1 683s Created read sampler 683s Sampling 3 reads 683s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 683s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 683s parsing sequence Sim.pm.1... 683s parsing sequence Sim.pm.2... 683s Parsed 143 reference bases 683s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 683s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 683s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 683s 3 reads; of these: 683s 3 (100.00%) were paired; of these: 683s 3 (100.00%) aligned concordantly 0 times 683s 0 (0.00%) aligned concordantly exactly 1 time 683s 0 (0.00%) aligned concordantly >1 times 683s ---- 683s 3 pairs aligned concordantly 0 times; of these: 683s 0 (0.00%) aligned discordantly 1 time 683s ---- 683s 3 pairs aligned 0 times concordantly or discordantly; of these: 683s 6 mates make up the pairs; of these: 683s 6 (100.00%) aligned 0 times 683s 0 (0.00%) aligned exactly 1 time 683s 0 (0.00%) aligned >1 times 683s 0.00% overall alignment rate 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s --- Summary --- 683s Read 1 reference strings 683s Checked 0 alignments, 0 edits 683s --------------- 683s PASSED 683s Flattened IUPAC characters 683s Mutating sequence Sim.pm.2 683s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 683s Finished SNPs 683s Finished ref gaps 683s Finished read gaps 683s Mutating sequence Sim.pm.1 683s Introducing 16 SNPs, 1/1 ref/read gaps, and 1 rearrangements 683s Finished SNPs 683s Finished ref gaps 683s Finished read gaps 683s Mutated reference genome to subject genome 683s SNPs introduced: 19 683s Reference gaps introduced: 2 683s Read gaps introduced: 1 683s Rearrangements introduced: 2 683s Created read sampler 683s Sampling 121 reads 683s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 683s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 683s parsing sequence Sim.pm.1... 683s parsing sequence Sim.pm.2... 683s Parsed 143 reference bases 683s *** Run 95 of 100 683s /usr/bin/bowtie2 -M 6 --n-ceil 0.925442380440702,1.32757357337687 --local --cp-ival 2 --trim3 2 --mp 6.85943371106492,3.74404518084779 --cp-min 9 --np 1 --score-min L,2.44410848186781,5.4697539116857 --gbar 2 --mm -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw 683s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 683s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '4' because it was < 2 characters long 683s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '15' because it was < 2 characters long 683s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '17' because it was < 2 characters long 683s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '37' because it was < 2 characters long 683s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '56' because it was < 2 characters long 683s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '78' because it was < 2 characters long 683s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '82' because it was < 2 characters long 683s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '89' because it was < 2 characters long 683s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 683s Warning: skipping read '93' because it was < 2 characters long 683s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '107' because it was < 2 characters long 683s 121 reads; of these: 683s 121 (100.00%) were unpaired; of these: 683s 121 (100.00%) aligned 0 times 683s 0 (0.00%) aligned exactly 1 time 683s 0 (0.00%) aligned >1 times 683s 0.00% overall alignment rate 683s Read 50 alignments... 683s Read 100 alignments... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s --- Summary --- 683s Read 1 reference strings 683s Checked 0 alignments, 0 edits 683s --------------- 683s PASSED 683s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 683s /usr/bin/bowtie2 -M 6 --n-ceil 0.925442380440702,1.32757357337687 --local --cp-ival 2 --trim3 2 --mp 6.85943371106492,3.74404518084779 --cp-min 9 --np 1 --score-min L,2.44410848186781,5.4697539116857 --gbar 2 --mm -r -p 4 -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 683s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 683s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '4' because it was < 2 characters long 683s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '15' because it was < 2 characters long 683s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '17' because it was < 2 characters long 683s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '37' because it was < 2 characters long 683s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '56' because it was < 2 characters long 683s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '78' because it was < 2 characters long 683s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '82' because it was < 2 characters long 683s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '89' because it was < 2 characters long 683s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 683s Warning: skipping read '93' because it was < 2 characters long 683s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 683s Warning: skipping read '107' because it was < 2 characters long 683s 121 reads; of these: 683s 121 (100.00%) were unpaired; of these: 683s 121 (100.00%) aligned 0 times 683s 0 (0.00%) aligned exactly 1 time 683s 0 (0.00%) aligned >1 times 683s 0.00% overall alignment rate 683s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 683s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 683s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 683s Flattened IUPAC characters 683s Mutating sequence Sim.pm.1 683s Introducing 15 SNPs, 0/1 ref/read gaps, and 1 rearrangements 683s Finished SNPs 683s Finished ref gaps 683s Finished read gaps 683s Mutating sequence Sim.pm.2 683s Introducing 2 SNPs, 2/1 ref/read gaps, and 2 rearrangements 683s Finished SNPs 683s Finished ref gaps 683s Finished read gaps 683s Mutated reference genome to subject genome 683s SNPs introduced: 17 683s Reference gaps introduced: 2 683s Read gaps introduced: 2 683s Rearrangements introduced: 3 683s Created read sampler 683s Sampling 64 reads 683s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 683s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 683s parsing sequence Sim.pm.1... 683s parsing sequence Sim.pm.2... 683s Parsed 143 reference bases 683s *** Run 96 of 100 683s /usr/bin/bowtie2 --mm --rdg 30.2712941477355 --score-min L,3.01463887060262,7.82162396369411 --np 1 --cp-min 8 -i S --mp 3.32924698432255,2.28224034653531 --cp-ival 2 --local -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 683s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '13' because it was < 2 characters long 683s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '27' because it was < 2 characters long 683s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '32' because it was < 2 characters long 683s 64 reads; of these: 683s 64 (100.00%) were paired; of these: 683s 64 (100.00%) aligned concordantly 0 times 683s 0 (0.00%) aligned concordantly exactly 1 time 683s 0 (0.00%) aligned concordantly >1 times 683s ---- 683s 64 pairs aligned concordantly 0 times; of these: 683s 0 (0.00%) aligned discordantly 1 time 683s ---- 683s 64 pairs aligned 0 times concordantly or discordantly; of these: 683s 128 mates make up the pairs; of these: 683s 128 (100.00%) aligned 0 times 683s 0 (0.00%) aligned exactly 1 time 683s 0 (0.00%) aligned >1 times 683s 0.00% overall alignment rate 683s Read 50 alignments... 683s Read 100 alignments... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s /usr/bin/bowtie2 --mm --rdg 30.2712941477355 --score-min L,3.01463887060262,7.82162396369411 --np 1 --cp-min 8 -i S --mp 3.32924698432255,2.28224034653531 --cp-ival 2 --local -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s Processing line... 683s --- Summary --- 683s Read 1 reference strings 683s Checked 0 alignments, 0 edits 683s --------------- 683s PASSED 683s ALSO checking that bowtie2 and bowtie2-align match up 683s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '13' because it was < 2 characters long 683s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #2 of read '27' because it was < 2 characters long 683s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 683s Warning: skipping mate #1 of read '32' because it was < 2 characters long 683s 64 reads; of these: 683s 64 (100.00%) were paired; of these: 683s 64 (100.00%) aligned concordantly 0 times 683s 0 (0.00%) aligned concordantly exactly 1 time 683s 0 (0.00%) aligned concordantly >1 times 683s ---- 683s 64 pairs aligned concordantly 0 times; of these: 683s 0 (0.00%) aligned discordantly 1 time 683s ---- 683s 64 pairs aligned 0 times concordantly or discordantly; of these: 683s 128 mates make up the pairs; of these: 683s 128 (100.00%) aligned 0 times 683s 0 (0.00%) aligned exactly 1 time 683s 0 (0.00%) aligned >1 times 683s 0.00% overall alignment rate 683s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 683s /usr/bin/bowtie2 --mm --rdg 30.2712941477355 --score-min L,3.01463887060262,7.82162396369411 --np 1 --cp-min 8 -i S --mp 3.32924698432255,2.28224034653531 --cp-ival 2 --local -r -p 2 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 683s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 684s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #2 of read '13' because it was < 2 characters long 684s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #2 of read '27' because it was < 2 characters long 684s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '32' because it was < 2 characters long 684s 64 reads; of these: 684s 64 (100.00%) were paired; of these: 684s 64 (100.00%) aligned concordantly 0 times 684s 0 (0.00%) aligned concordantly exactly 1 time 684s 0 (0.00%) aligned concordantly >1 times 684s ---- 684s 64 pairs aligned concordantly 0 times; of these: 684s 0 (0.00%) aligned discordantly 1 time 684s ---- 684s 64 pairs aligned 0 times concordantly or discordantly; of these: 684s 128 mates make up the pairs; of these: 684s 128 (100.00%) aligned 0 times 684s 0 (0.00%) aligned exactly 1 time 684s 0sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 684s (0.00%) aligned >1 times 684s 0.00% overall alignment rate 684s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 684s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 684s *** Run 97 of 100 684s /usr/bin/bowtie2 --rfg 18.5883908728199,10.4930738741119 --mp 5.92515401106239,4.94927216213575 -N 1 -L23 --score-min L,6.2260340881594,7.32907971459058 --trim3 6 --cp-ival 2 --local --trim5 2 --np 3 --cp-min 3 -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw 684s Flattened IUPAC characters 684s Mutating sequence Sim.pm.2 684s Introducing 14 SNPs, 1/2 ref/read gaps, and 0 rearrangements 684s Finished SNPs 684s Finished ref gaps 684s Finished read gaps 684s Mutating sequence Sim.pm.1 684s Introducing 10 SNPs, 1/1 ref/read gaps, and 1 rearrangements 684s Finished SNPs 684s Finished ref gaps 684s Finished read gaps 684s Mutated reference genome to subject genome 684s SNPs introduced: 24 684s Reference gaps introduced: 2 684s Read gaps introduced: 3 684s Rearrangements introduced: 1 684s Created read sampler 684s Sampling 74 reads 684s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 684s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 684s parsing sequence Sim.pm.1... 684s parsing sequence Sim.pm.2... 684s Parsed 143 reference bases 684s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '17' because it was < 2 characters long 684s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '19' because it was < 2 characters long 684s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '24' because it was < 2 characters long 684s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '25' because it was < 2 characters long 684s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '26' because it was < 2 characters long 684s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '34' because it was < 2 characters long 684s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '36' because it was < 2 characters long 684s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '37' because it was < 2 characters long 684s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '48' because it was < 2 characters long 684s Warning: skipping read '51' because length (1) <= # seed mismatches (1) 684s Warning: skipping read '51' because it was < 2 characters long 684s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '53' because it was < 2 characters long 684s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '58' because it was < 2 characters long 684s Warning: skipping read '60' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '60' because it was < 2 characters long 684s Warning: skipping read '61' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '61' because it was < 2 characters long 684s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '67' because it was < 2 characters long 684s Warning: skipping read '71' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '71' because it was < 2 characters long 684s 74 reads; of these: 684s 74 (100.00%) were unpaired; of these: 684s 74 (100.00%) aligned 0 times 684s 0 (0.00%) aligned exactly 1 time 684s 0 (0.00%) aligned >1 times 684s 0.00% overall alignment rate 684s Read 50 alignments... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s /usr/bin/bowtie2 --rfg 18.5883908728199,10.4930738741119 --mp 5.92515401106239,4.94927216213575 -N 1 -L23 --score-min L,6.2260340881594,7.32907971459058 --trim3 6 --cp-ival 2 --local --trim5 2 --np 3 --cp-min 3 -r -x /tmp/Sim.pm.HBgkkIzX /tmp/Sim.pm.HBgkkIzX_1.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.als 684s Processing line... 684s Processing line... 684s Processing line... 684s --- Summary --- 684s Read 1 reference strings 684s Checked 0 alignments, 0 edits 684s --------------- 684s PASSED 684s ALSO checking that bowtie2 and bowtie2-align match up 684s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '17' because it was < 2 characters long 684s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '19' because it was < 2 characters long 684s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '24' because it was < 2 characters long 684s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '25' because it was < 2 characters long 684s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '26' because it was < 2 characters long 684s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '34' because it was < 2 characters long 684s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '36' because it was < 2 characters long 684s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '37' because it was < 2 characters long 684s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '48' because it was < 2 characters long 684s Warning: skipping read '51' because length (1) <= # seed mismatches (1) 684s Warning: skipping read '51' because it was < 2 characters long 684s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '53' because it was < 2 characters long 684s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '58' because it was < 2 characters long 684s Warning: skipping read '60' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '60' because it was < 2 characters long 684s Warning: skipping read '61' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '61' because it was < 2 characters long 684s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '67' because it was < 2 characters long 684s Warning: skipping read '71' because length (0) <= # seed mismatches (1) 684s Warning: skipping read '71' because it was < 2 characters long 684s diff -uw /tmp/Sim.pm.HBgkkIzX.als /tmp/Sim.pm.HBgkkIzX.debug.als 684s 74 reads; of these: 684s 74 (100.00%) were unpaired; of these: 684s 74 (100.00%) aligned 0 times 684s 0 (0.00%) aligned exactly 1 time 684s 0 (0.00%) aligned >1 times 684s 0.00% overall alignment rate 684s Flattened IUPAC characters 684s Mutating sequence Sim.pm.2 684s Introducing 14 SNPs, 1/0 ref/read gaps, and 3 rearrangements 684s Finished SNPs 684s Finished ref gaps 684s Finished read gaps 684s Mutating sequence Sim.pm.1 684s Introducing 14 SNPs, 0/1 ref/read gaps, and 0 rearrangements 684s Finished SNPs 684s Finished ref gaps 684s Finished read gaps 684s Mutated reference genome to subject genome 684s SNPs introduced: 28 684s Reference gaps introduced: 1 684s Read gaps introduced: 1 684s Rearrangements introduced: 3 684s Created read sampler 684s Sampling 141 reads 684s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.fastq & /tmp/Sim.pm.HBgkkIzX_2.fastq 684s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 684s *** Run 98 of 100 684s /usr/bin/bowtie2 --nofw -i L,0.313373631395753 --mp 9.07408631141174,2.98614544459729 -N 0 -L20 --local --cp-ival 1 -a --norc --n-ceil 0.217318143682574,0.89575008518936 --rdg 38.3445164679009,16.0198520397243 --mm --score-min L,6.58895571579283,3.94729870488885 --gbar 1 --cp-min 2 -q -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq 684s parsing sequence Sim.pm.1... 684s parsing sequence Sim.pm.2... 684s Parsed 143 reference bases 684s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #2 of read '24' because it was < 2 characters long 684s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #2 of read '25' because it was < 2 characters long 684s Warning: skipping mate #1 of read '60' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '60' because it was < 2 characters long 684s Read 50 alignments... 684s Read 100 alignments... 684s Read 150 alignments... 684s 141 reads; of these: 684s 141 (100.00%) were paired; of these: 684s 141 (100.00%) aligned concordantly 0 times 684s 0 (0.00%) aligned concordantly exactly 1 time 684s 0 (0.00%) aligned concordantly >1 times 684s ---- 684s 141 pairs aligned concordantly 0 times; of these: 684s 0 (0.00%) aligned discordantly 1 time 684s ---- 684s 141 pairs aligned 0 times concordantly or discordantly; of these: 684s 282 mates make up the pairs; of these: 684s 282 (100.00%) aligned 0 times 684s 0 (0.00%) aligned exactly 1 time 684s 0 (0.00%) aligned >1 times 684s 0.00% overall alignment rate 684s Read 200 alignments... 684s Read 250 alignments... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s 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line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s /usr/bin/bowtie2 --nofw -i L,0.313373631395753 --mp 9.07408631141174,2.98614544459729 -N 0 -L20 --local --cp-ival 1 -a --norc --n-ceil 0.217318143682574,0.89575008518936 --rdg 38.3445164679009,16.0198520397243 --mm --score-min L,6.58895571579283,3.94729870488885 --gbar 1 --cp-min 2 -q -p 2 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.fastq -2 /tmp/Sim.pm.HBgkkIzX_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s --- Summary --- 684s Read 1 reference strings 684s Checked 0 alignments, 0 edits 684s --------------- 684s PASSED 684s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 684s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #2 of read '24' because it was < 2 characters long 684s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #2 of read '25' because it was < 2 characters long 684s Warning: skipping mate #1 of read '60' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '60' because it was < 2 characters long 684s 141 reads; of these: 684s 141 (100.00%) were paired; of these: 684s 141 (100.00%) aligned concordantly 0 times 684s 0 (0.00%) aligned concordantly exactly 1 time 684s 0 (0.00%) aligned concordantly >1 times 684s ---- 684s 141 pairs aligned concordantly 0 times; of these: 684s 0 (0.00%) aligned discordantly 1 time 684s ---- 684s 141 pairs aligned 0 times concordantly or discordantly; of these: 684s 282 mates make up the pairs; of these: 684s 282 (100.00%) aligned 0 times 684s 0 (0.00%) aligned exactly 1 time 684s 0 (0.00%) aligned >1 times 684s 0.00% overall alignment rate 684s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 684s Flattened IUPAC characters 684s Mutating sequence Sim.pm.2 684s Introducing 11 SNPs, 3/0 ref/read gaps, and 1 rearrangements 684s Finished SNPs 684s Finished ref gaps 684s Finished read gaps 684s Mutating sequence Sim.pm.1 684s Introducing 21 SNPs, 1/1 ref/read gaps, and 0 rearrangements 684s Finished SNPs 684s Finished ref gaps 684s Finished read gaps 684s Mutated reference genome to subject genome 684s SNPs introduced: 32 684s Reference gaps introduced: 4 684s Read gaps introduced: 1 684s Rearrangements introduced: 1 684s Created read sampler 684s Sampling 38 reads 684s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.raw & /tmp/Sim.pm.HBgkkIzX_2.raw 684s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 684s parsing sequence Sim.pm.1... 684s parsing sequence Sim.pm.2... 684s Parsed 143 reference bases 684s *** Run 99 of 100 684s /usr/bin/bowtie2 --cp-min 4 --n-ceil 0.0604160375126466,1.31904044287207 --trim5 8 --cp-ival 2 --trim3 2 --score-min L,5.3821486409207,4.75773178665303 --mp 7.98243487277393,2.28498621621347 -D 9 --rdg 37.5315129692567 --mm --rfg 44.2330064917009 -r -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw 684s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 684s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '1' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 684s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '7' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 684s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '9' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 684s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '25' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 684s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '32' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 684s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '35' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 684s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #2 of read '37' because it was < 2 characters long 684s 38 reads; of these: 684s 31 (81.58%) were paired; of these: 684s 31 (100.00%) aligned concordantly 0 times 684s 0 (0.00%) aligned concordantly exactly 1 time 684s 0 (0.00%) aligned concordantly >1 times 684s ---- 684s 31 pairs aligned concordantly 0 times; of these: 684s 0 (0.00%) aligned discordantly 1 time 684s ---- 684s 31 pairs aligned 0 times concordantly or discordantly; of these: 684s 62 mates make up the pairs; of these: 684s 55 (88.71%) aligned 0 times 684s 5 (8.06%) aligned exactly 1 time 684s 2 (3.23%) aligned >1 times 684s 7 (18.42%) were unpaired; of these: 684s 5 (71.43%) aligned 0 times 684s 1 (14.29%) aligned exactly 1 time 684s 1 (14.29%) aligned >1 times 684s 13.04% overall alignment rate 684s Read 50 alignments... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s GGGGA 684s GGGGA 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s CCCAGCTTAGGCGGTCAG 684s CCCAGCTTAGGCGGTCAG 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s TGC 684s TGC 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s GAGAGGGTGA 684s GAGAGGGTGA 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s GTAGGGG 684s GTAGGGG 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s GGG 684s GGG 684s Processing line... 684s Processing line... 684s Processing line... 684s CT 684s CT 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s GGGGG 684s GGGGG 684s Processing line... 684s Processing line... 684s TGCGCCCAGCTTAGGCGGTCAGGAGGGA 684s TGCGCCCAGCTTAGGCGGTCAGGAGGGA 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s --- Summary --- 684s Read 1 reference strings 684s Checked 9 alignments, 0 edits 684s --------------- 684s /usr/bin/bowtie2 --cp-min 4 --n-ceil 0.0604160375126466,1.31904044287207 --trim5 8 --cp-ival 2 --trim3 2 --score-min L,5.3821486409207,4.75773178665303 --mp 7.98243487277393,2.28498621621347 -D 9 --rdg 37.5315129692567 --mm --rfg 44.2330064917009 -r -p 4 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.raw -2 /tmp/Sim.pm.HBgkkIzX_2.raw | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 684s PASSED 684s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 684s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 684s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '1' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 684s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '7' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 684s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '9' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 684s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '25' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 684s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '32' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 684s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read '35' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 684s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #2 of read '37' because it was < 2 characters long 684s 38 reads; of these: 684s 31 (81.58%) were paired; of these: 684s 31 (100.00%) aligned concordantly 0 times 684s 0 (0.00%) aligned concordantly exactly 1 time 684s 0 (0.00%) aligned concordantly >1 times 684s ---- 684s 31 pairs aligned concordantly 0 times; of these: 684s 0 (0.00%) aligned discordantly 1 time 684s ---- 684s 31 pairs aligned 0 times concordantly or discordantly; of these: 684s 62 mates make up the pairs; of these: 684s 55 (88.71%) aligned 0 times 684s 5 (8.06%) aligned exactly 1 time 684s 2 (3.23%) aligned >1 times 684s 7 (18.42%) were unpaired; of these: 684s 5 (71.43%) aligned 0 times 684s 1 (14.29%) aligned exactly 1 time 684s 1 (14.29%) aligned >1 times 684s 13.04% overall alignment rate 684s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 684s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 684s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 684s Flattened IUPAC characters 684s Mutating sequence Sim.pm.1 684s Introducing 2 SNPs, 0/3 ref/read gaps, and 3 rearrangements 684s Finished SNPs 684s Finished ref gaps 684s Finished read gaps 684s Mutating sequence Sim.pm.2 684s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 684s Finished SNPs 684s Finished ref gaps 684s Finished read gaps 684s Mutated reference genome to subject genome 684s SNPs introduced: 9 684s Reference gaps introduced: 0 684s Read gaps introduced: 4 684s Rearrangements introduced: 3 684s Created read sampler 684s Sampling 54 reads 684s Dumping reads to temporary files /tmp/Sim.pm.HBgkkIzX_1.qseq & /tmp/Sim.pm.HBgkkIzX_2.qseq 684s Parsing FASTA file /tmp/Sim.pm.HBgkkIzX.fa... 684s parsing sequence Sim.pm.1... 684s *** Run 100 of 100 684s /usr/bin/bowtie2 --mm --rdg 40.084858806903 -R 2 --score-min L,4.424251590884,7.85995834371842 --cp-ival 1 --cp-min 13 -M 2 --qseq -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq 684s parsing sequence Sim.pm.2... 684s Parsed 143 reference bases 684s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 684s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 684s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 684s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 684s 54 reads; of these: 684s 54 (100.00%) were paired; of these: 684s 52 (96.30%) aligned concordantly 0 times 684s 1 (1.85%) aligned concordantly exactly 1 time 684s 1 (1.85%) aligned concordantly >1 times 684s ---- 684s 52 pairs aligned concordantly 0 times; of these: 684s 0 (0.00%) aligned discordantly 1 time 684s ---- 684s 52 pairs aligned 0 times concordantly or discordantly; of these: 684s 104 mates make up the pairs; of these: 684s 89 (85.58%) aligned 0 times 684s 14 (13.46%) aligned exactly 1 time 684s 1 (0.96%) aligned >1 times 684s 17.59% overall alignment rate 684s Read 50 alignments... 684s Read 100 alignments... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s GTGGTAGGGGGGGACTGG 684s GTGGTAGGGGGGGACTGG 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s TTGAGAGGGTGACAGAGGCGT 684s TTGAGAGGGTGACAGAGGCGT 684s Processing line... 684s Processing line... 684s AGGGG 684s AGGGG 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s /usr/bin/bowtie2 --mm --rdg 40.084858806903 -R 2 --score-min L,4.424251590884,7.85995834371842 --cp-ival 1 --cp-min 13 -M 2 --qseq -p 4 -x /tmp/Sim.pm.HBgkkIzX -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als 684s Processing line... 684s Processing line... 684s TGAGAGGGTGA 684s TGAGAGGGTGA 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s GGGTGGTGTTGAG 684s GGGTGGTGTTGAG 684s Processing line... 684s GAGGCGTGG 684s GAGGCGTGG 684s Processing line... 684s GGGGGA 684s GGGGGA 684s Processing line... 684s Processing line... 684s GGTGTTGAGAGGGTGACAGAGGCGTG 684s GGTGTTGAGAGGGTGACAGAGGCGTG 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s GAGAG 684s GAGAG 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s GGTGGTAGGGGGGGAC 684s GGTGGTAGGGGGGGAC 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s TCC 684s TCC 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s CTGGTGGTGGTAGGG 684s CTGGTGGTGGTAGGG 684s Processing line... 684s Processing line... 684s GAGGGTGA 684s GAGGGTGA 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s TGGTGTTGAGAGGG 684s TGGTGTTGAGAGGG 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s TGTTGAGA 684s TGTTGAGA 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s CCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGCTGG 684s CCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGGAGCTGG 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s CCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGG 684s CCGCGGCTCGGTCTGCGCCCAGCTTAGGCGGTCAGGAGGG 684s Processing line... 684s Processing line... 684s CTGCGCCCAGCTTAGGCGGTCAGG 684s CTGCGCCCAGCTTAGGCGGTCAGG 684s Processing line... 684s GGTGGTAGGGGGGGACTGGC 684s GGTGGTAGGGGGGGACTGGC 684s Processing line... 684s Processing line... 684s Processing line... 684s Processing line... 684s --- Summary --- 684s Read 1 reference strings 684s Checked 19 alignments, 0 edits 684s --------------- 684s PASSED 684s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 685s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 685s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 685s 54 reads; of these: 685s 54 (100.00%) were paired; of these: 685s 52 (96.30%) aligned concordantly 0 times 685s 1 (1.85%) aligned concordantly exactly 1 time 685s 1 (1.85%) aligned concordantly >1 times 685s ---- 685s 52 pairs aligned concordantly 0 times; of these: 685s 0 (0.00%) aligned discordantly 1 time 685s ---- 685s 52 pairs aligned 0 times concordantly or discordantly; of these: 685s 104 mates make up the pairs; of these: 685s 89 (85.58%) aligned 0 times 685s 14 (13.46%) aligned exactly 1 time 685s 1 (0.96%) aligned >1 times 685s 17.59% overall alignment rate 685s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.px.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.als.sorted 685s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.HBgkkIzX.debug.als | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.debug.als.sorted 685s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als.sorted /tmp/Sim.pm.HBgkkIzX.px.als.sorted 685s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 685s /usr/bin/bowtie2 --mm --rdg 40.084858806903 -R 2 --score-min L,4.424251590884,7.85995834371842 --cp-ival 1 --cp-min 13 -M 2 --qseq -p 3 -x /tmp/Sim.pm.HBgkkIzX --reorder -1 /tmp/Sim.pm.HBgkkIzX_1.qseq -2 /tmp/Sim.pm.HBgkkIzX_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.HBgkkIzX.px.reord.als 685s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 685s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 685s 54 reads; of these: 685s 54 (100.00%) were paired; of these: 685s 52 (96.30%) aligned concordantly 0 times 685s 1 (1.85%) aligned concordantly exactly 1 time 685s 1 (1.85%) aligned concordantly >1 times 685s ---- 685s 52 pairs aligned concordantly 0 times; of these: 685s 0 (0.00%) aligned discordantly 1 time 685s ---- 685s 52 pairs aligned 0 times concordantly or discordantly; of these: 685s 104 mates make up the pairs; of these: 685s 89 (85.58%) aligned 0 times 685s 14 (13.46%) aligned exactly 1 time 685s 1 (0.96%) aligned >1 times 685s 17.59% overall alignment rate 685s diff -uw /tmp/Sim.pm.HBgkkIzX.debug.als /tmp/Sim.pm.HBgkkIzX.px.reord.als 685s Created DNA generator 685s N frac: 0.009 685s IUPAC frac: 0.010 685s AT/ACGT frac: 0.328 685s A/AT frac: 0.269 685s C/CG frac: 0.283 685s Generating 2 references 685s Generated reference 'Sim.pm.1' of untrimmed length 297, trimmed length 87 685s Generated reference 'Sim.pm.2' of untrimmed length 281, trimmed length 147 685s Wrote references to /tmp/Sim.pm.RKKEKvBt.fa 685s A: 13 685s C: 52 685s G: 101 685s M: 1 685s N: 1 685s T: 65 685s W: 1 685s Executing: /usr/bin/bowtie2-build --large-index --threads 1 /tmp/Sim.pm.RKKEKvBt.fa /tmp/Sim.pm.RKKEKvBt 685s *** TEST CASE *** 685s Settings: 685s Output files: "/tmp/Sim.pm.RKKEKvBt.*.bt2l" 685s Line rate: 7 (line is 128 bytes) 685s Lines per side: 1 (side is 128 bytes) 685s Offset rate: 4 (one in 16) 685s FTable chars: 10 685s Strings: unpacked 685s Max bucket size: default 685s Max bucket size, sqrt multiplier: default 685s Max bucket size, len divisor: 4 685s Difference-cover sample period: 1024 685s Endianness: little 685s Actual local endianness: little 685s Sanity checking: disabled 685s Assertions: disabled 685s Random seed: 0 685s Sizeofs: void*:8, int:4, long:8, size_t:8 685s Input files DNA, FASTA: 685s /tmp/Sim.pm.RKKEKvBt.fa 685s Reading reference sizes 685s Time reading reference sizes: 00:00:00 685s Calculating joined length 685s Writing header 685s Reserving space for joined string 685s Joining reference sequences 685s Time to join reference sequences: 00:00:00 685s bmax according to bmaxDivN setting: 57 685s Using parameters --bmax 43 --dcv 1024 685s Doing ahead-of-time memory usage test 685s Building a LARGE index 685s Passed! Constructing with these parameters: --bmax 43 --dcv 1024 685s Constructing suffix-array element generator 685s Building DifferenceCoverSample 685s Building sPrime 685s Building sPrimeOrder 685s V-Sorting samples 685s V-Sorting samples time: 00:00:00 685s Allocating rank array 685s Ranking v-sort output 685s Ranking v-sort output time: 00:00:00 685s Invoking Larsson-Sadakane on ranks 685s Invoking Larsson-Sadakane on ranks time: 00:00:00 685s Sanity-checking and returning 685s Building samples 685s Reserving space for 12 sample suffixes 685s Generating random suffixes 685s QSorting 12 sample offsets, eliminating duplicates 685s QSorting sample offsets, eliminating duplicates time: 00:00:00 685s Multikey QSorting 12 samples 685s (Using difference cover) 685s Multikey QSorting samples time: 00:00:00 685s Calculating bucket sizes 685s Splitting and merging 685s Splitting and merging time: 00:00:00 685s Avg bucket size: 32.1429 (target: 42) 685s Converting suffix-array elements to index image 685s Allocating ftab, absorbFtab 685s Entering Ebwt loop 685s Getting block 1 of 7 685s Reserving size (43) for bucket 1 685s Calculating Z arrays for bucket 1 685s Entering block accumulator loop for bucket 1: 685s bucket 1: 10% 685s bucket 1: 20% 685s bucket 1: 30% 685s bucket 1: 40% 685s bucket 1: 50% 685s bucket 1: 60% 685s bucket 1: 70% 685s bucket 1: 80% 685s bucket 1: 90% 685s bucket 1: 100% 685s Sorting block of length 33 for bucket 1 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 34 for bucket 1 685s Getting block 2 of 7 685s Reserving size (43) for bucket 2 685s Calculating Z arrays for bucket 2 685s Entering block accumulator loop for bucket 2: 685s bucket 2: 10% 685s bucket 2: 20% 685s bucket 2: 30% 685s bucket 2: 40% 685s bucket 2: 50% 685s bucket 2: 60% 685s bucket 2: 70% 685s bucket 2: 80% 685s bucket 2: 90% 685s bucket 2: 100% 685s Sorting block of length 38 for bucket 2 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 39 for bucket 2 685s Getting block 3 of 7 685s Reserving size (43) for bucket 3 685s Calculating Z arrays for bucket 3 685s Entering block accumulator loop for bucket 3: 685s bucket 3: 10% 685s bucket 3: 20% 685s bucket 3: 30% 685s bucket 3: 40% 685s bucket 3: 50% 685s bucket 3: 60% 685s bucket 3: 70% 685s bucket 3: 80% 685s bucket 3: 90% 685s bucket 3: 100% 685s Sorting block of length 31 for bucket 3 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 32 for bucket 3 685s Getting block 4 of 7 685s Reserving size (43) for bucket 4 685s Calculating Z arrays for bucket 4 685s Entering block accumulator loop for bucket 4: 685s bucket 4: 10% 685s bucket 4: 20% 685s bucket 4: 30% 685s bucket 4: 40% 685s bucket 4: 50% 685s bucket 4: 60% 685s bucket 4: 70% 685s bucket 4: 80% 685s bucket 4: 90% 685s bucket 4: 100% 685s Sorting block of length 39 for bucket 4 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 40 for bucket 4 685s Getting block 5 of 7 685s Reserving size (43) for bucket 5 685s Calculating Z arrays for bucket 5 685s Entering block accumulator loop for bucket 5: 685s bucket 5: 10% 685s bucket 5: 20% 685s bucket 5: 30% 685s bucket 5: 40% 685s bucket 5: 50% 685s bucket 5: 60% 685s bucket 5: 70% 685s bucket 5: 80% 685s bucket 5: 90% 685s bucket 5: 100% 685s Sorting block of length 35 for bucket 5 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 36 for bucket 5 685s Getting block 6 of 7 685s Reserving size (43) for bucket 6 685s Calculating Z arrays for bucket 6 685s Entering block accumulator loop for bucket 6: 685s bucket 6: 10% 685s bucket 6: 20% 685s bucket 6: 30% 685s bucket 6: 40% 685s bucket 6: 50% 685s bucket 6: 60% 685s bucket 6: 70% 685s bucket 6: 80% 685s bucket 6: 90% 685s bucket 6: 100% 685s Sorting block of length 10 for bucket 6 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 11 for bucket 6 685s Getting block 7 of 7 685s Reserving size (43) for bucket 7 685s Calculating Z arrays for bucket 7 685s Entering block accumulator loop for bucket 7: 685s bucket 7: 10% 685s bucket 7: 20% 685s bucket 7: 30% 685s bucket 7: 40% 685s bucket 7: 50% 685s bucket 7: 60% 685s bucket 7: 70% 685s bucket 7: 80% 685s bucket 7: 90% 685s bucket 7: 100% 685s Sorting block of length 39 for bucket 7 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 40 for bucket 7 685s Exited Ebwt loop 685s fchr[A]: 0 685s fchr[C]: 13 685s fchr[G]: 65 685s fchr[T]: 166 685s fchr[$]: 231 685s Exiting Ebwt::buildToDisk() 685s Returning from initFromVector 685s Wrote 8389155 bytes to primary EBWT file: /tmp/Sim.pm.RKKEKvBt.1.bt2l.tmp 685s Wrote 124 bytes to secondary EBWT file: /tmp/Sim.pm.RKKEKvBt.2.bt2l.tmp 685s Re-opening _in1 and _in2 as input streams 685s Returning from Ebwt constructor 685s Headers: 685s len: 231 685s bwtLen: 232 685s sz: 58 685s bwtSz: 58 685s lineRate: 7 685s offRate: 4 685s offMask: 0xfffffffffffffff0 685s ftabChars: 10 685s eftabLen: 20 685s eftabSz: 160 685s ftabLen: 1048577 685s ftabSz: 8388616 685s offsLen: 15 685s offsSz: 120 685s lineSz: 128 685s sideSz: 128 685s sideBwtSz: 96 685s sideBwtLen: 384 685s numSides: 1 685s numLines: 1 685s ebwtTotLen: 128 685s ebwtTotSz: 128 685s color: 0 685s reverse: 0 685s Total time for call to driver() for forward index: 00:00:00 685s Reading reference sizes 685s Time reading reference sizes: 00:00:00 685s Calculating joined length 685s Writing header 685s Reserving space for joined string 685s Joining reference sequences 685s Time to join reference sequences: 00:00:00 685s Time to reverse reference sequence: 00:00:00 685s bmax according to bmaxDivN setting: 57 685s Using parameters --bmax 43 --dcv 1024 685s Doing ahead-of-time memory usage test 685s Passed! Constructing with these parameters: --bmax 43 --dcv 1024 685s Constructing suffix-array element generator 685s Building DifferenceCoverSample 685s Building sPrime 685s Building sPrimeOrder 685s V-Sorting samples 685s V-Sorting samples time: 00:00:00 685s Allocating rank array 685s Ranking v-sort output 685s Ranking v-sort output time: 00:00:00 685s Invoking Larsson-Sadakane on ranks 685s Invoking Larsson-Sadakane on ranks time: 00:00:00 685s Sanity-checking and returning 685s Building samples 685s Reserving space for 12 sample suffixes 685s Generating random suffixes 685s QSorting 12 sample offsets, eliminating duplicates 685s QSorting sample offsets, eliminating duplicates time: 00:00:00 685s Multikey QSorting 12 samples 685s (Using difference cover) 685s Multikey QSorting samples time: 00:00:00 685s Calculating bucket sizes 685s Splitting and merging 685s Splitting and merging time: 00:00:00 685s Avg bucket size: 37.6667 (target: 42) 685s Converting suffix-array elements to index image 685s Allocating ftab, absorbFtab 685s Entering Ebwt loop 685s Getting block 1 of 6 685s Reserving size (43) for bucket 1 685s Calculating Z arrays for bucket 1 685s Entering block accumulator loop for bucket 1: 685s bucket 1: 10% 685s bucket 1: 20% 685s bucket 1: 30% 685s bucket 1: 40% 685s bucket 1: 50% 685s bucket 1: 60% 685s bucket 1: 70% 685s bucket 1: 80% 685s bucket 1: 90% 685s bucket 1: 100% 685s Sorting block of length 42 for bucket 1 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 43 for bucket 1 685s Getting block 2 of 6 685s Reserving size (43) for bucket 2 685s Calculating Z arrays for bucket 2 685s Entering block accumulator loop for bucket 2: 685s bucket 2: 10% 685s bucket 2: 20% 685s bucket 2: 30% 685s bucket 2: 40% 685s bucket 2: 50% 685s bucket 2: 60% 685s bucket 2: 70% 685s bucket 2: 80% 685s bucket 2: 90% 685s bucket 2: 100% 685s Sorting block of length 39 for bucket 2 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 40 for bucket 2 685s Getting block 3 of 6 685s Reserving size (43) for bucket 3 685s Calculating Z arrays for bucket 3 685s Entering block accumulator loop for bucket 3: 685s bucket 3: 10% 685s bucket 3: 20% 685s bucket 3: 30% 685s bucket 3: 40% 685s bucket 3: 50% 685s bucket 3: 60% 685s bucket 3: 70% 685s bucket 3: 80% 685s bucket 3: 90% 685s bucket 3: 100% 685s Sorting block of length 40 for bucket 3 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 41 for bucket 3 685s Getting block 4 of 6 685s Reserving size (43) for bucket 4 685s Calculating Z arrays for bucket 4 685s Entering block accumulator loop for bucket 4: 685s bucket 4: 10% 685s bucket 4: 20% 685s bucket 4: 30% 685s bucket 4: 40% 685s bucket 4: 50% 685s bucket 4: 60% 685s bucket 4: 70% 685s bucket 4: 80% 685s bucket 4: 90% 685s bucket 4: 100% 685s Sorting block of length 41 for bucket 4 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 42 for bucket 4 685s Getting block 5 of 6 685s Reserving size (43) for bucket 5 685s Calculating Z arrays for bucket 5 685s Entering block accumulator loop for bucket 5: 685s bucket 5: 10% 685s bucket 5: 20% 685s bucket 5: 30% 685s bucket 5: 40% 685s bucket 5: 50% 685s bucket 5: 60% 685s bucket 5: 70% 685s bucket 5: 80% 685s bucket 5: 90% 685s bucket 5: 100% 685s Sorting block of length 42 for bucket 5 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 43 for bucket 5 685s Getting block 6 of 6 685s Reserving size (43) for bucket 6 685s Calculating Z arrays for bucket 6 685s Entering block accumulator loop for bucket 6: 685s bucket 6: 10% 685s bucket 6: 20% 685s bucket 6: 30% 685s bucket 6: 40% 685s bucket 6: 50% 685s bucket 6: 60% 685s bucket 6: 70% 685s bucket 6: 80% 685s bucket 6: 90% 685s bucket 6: 100% 685s Sorting block of length 22 for bucket 6 685s (Using difference cover) 685s Sorting block time: 00:00:00 685s Returning block of 23 for bucket 6 685s Exited Ebwt loop 685s fchr[A]: 0 685s fchr[C]: 13 685s fchr[G]: 65 685s fchr[T]: 166 685s fchr[$]: 231 685s Exiting Ebwt::buildToDisk() 685s Returning from initFromVector 685s Wrote 8389155 bytes to primary EBWT file: /tmp/Sim.pm.RKKEKvBt.rev.1.bt2l.tmp 685s Wrote 124 bytes to secondary EBWT file: /tmp/Sim.pm.RKKEKvBt.rev.2.bt2l.tmp 685s Re-opening _in1 and _in2 as input streams 685s Returning from Ebwt constructor 685s Headers: 685s len: 231 685s bwtLen: 232 685s sz: 58 685s bwtSz: 58 685s lineRate: 7 685s offRate: 4 685s offMask: 0xfffffffffffffff0 685s ftabChars: 10 685s eftabLen: 20 685s eftabSz: 160 685s ftabLen: 1048577 685s ftabSz: 8388616 685s offsLen: 15 685s offsSz: 120 685s lineSz: 128 685s sideSz: 128 685s sideBwtSz: 96 685s sideBwtLen: 384 685s numSides: 1 685s numLines: 1 685s ebwtTotLen: 128 685s ebwtTotSz: 128 685s color: 0 685s reverse: 1 685s Total time for backward call to driver() for mirror index: 00:00:00 685s Renaming /tmp/Sim.pm.RKKEKvBt.3.bt2l.tmp to /tmp/Sim.pm.RKKEKvBt.3.bt2l 685s Renaming /tmp/Sim.pm.RKKEKvBt.4.bt2l.tmp to /tmp/Sim.pm.RKKEKvBt.4.bt2l 685s Renaming /tmp/Sim.pm.RKKEKvBt.1.bt2l.tmp to /tmp/Sim.pm.RKKEKvBt.1.bt2l 685s Renaming /tmp/Sim.pm.RKKEKvBt.2.bt2l.tmp to /tmp/Sim.pm.RKKEKvBt.2.bt2l 685s Renaming /tmp/Sim.pm.RKKEKvBt.rev.1.bt2l.tmp to /tmp/Sim.pm.RKKEKvBt.rev.1.bt2l 685s Renaming /tmp/Sim.pm.RKKEKvBt.rev.2.bt2l.tmp to /tmp/Sim.pm.RKKEKvBt.rev.2.bt2l 685s Built nucleotide index '/tmp/Sim.pm.RKKEKvBt' 685s Flattened IUPAC characters 685s Mutating sequence Sim.pm.2 685s Introducing 24 SNPs, 0/2 ref/read gaps, and 0 rearrangements 685s Finished SNPs 685s Finished ref gaps 685s Finished read gaps 685s Mutating sequence Sim.pm.1 685s Introducing 9 SNPs, 2/0 ref/read gaps, and 3 rearrangements 685s Finished SNPs 685s Finished ref gaps 685s Finished read gaps 685s Mutated reference genome to subject genome 685s SNPs introduced: 33 685s Reference gaps introduced: 2 685s Read gaps introduced: 2 685s Rearrangements introduced: 3 685s Created read sampler 685s Sampling 29 reads 685s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 685s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 685s parsing sequence Sim.pm.1... 685s parsing sequence Sim.pm.2... 685s *** Run 1 of 100 685s /usr/bin/bowtie2 --mp 4.07855984181053,2.82592316307289 -i C,0.488861429762664,1.26665401350036 -R 3 -D 41 --score-min L,8.47248584924326,2.4148052131098 --mm --norc --cp-min 3 --np 1 --large-index --cp-ival 5 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 685s Parsed 234 reference bases 685s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 685s 29 reads; of these: 685s 29 (100.00%) were unpaired; of these: 685s 24 (82.76%) aligned 0 times 685s 2 (6.90%) aligned exactly 1 time 685s 3 (10.34%) aligned >1 times 685s 17.24% overall alignment rate 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TTGGTGT 685s TTGGTGT 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCC 685s TCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCC 685s Processing line... 685s Processing line... 685s GG 685s GG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GTTGTAGGCCGTTGGG 685s GTTGTAGGCCGTTGGG 685s Processing line... 685s GTTGTAG 685s GTTGTAG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s --- Summary --- 685s Read 1 reference strings 685s Checked 5 alignments, 0 edits 685s --------------- 685s PASSED 685s ALSO checking that bowtie2 and bowtie2-align match up 685s /usr/bin/bowtie2 --mp 4.07855984181053,2.82592316307289 -i C,0.488861429762664,1.26665401350036 -R 3 -D 41 --score-min L,8.47248584924326,2.4148052131098 --mm --norc --cp-min 3 --np 1 --large-index --cp-ival 5 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 685s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 685s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 685s 29 reads; of these: 685s 29 (100.00%) were unpaired; of these: 685s 24 (82.76%) aligned 0 times 685s 2 (6.90%) aligned exactly 1 time 685s 3 (10.34%) aligned >1 times 685s 17.24% overall alignment rate 685s Flattened IUPAC characters 685s Mutating sequence Sim.pm.1 685s Introducing 7 SNPs, 0/2 ref/read gaps, and 3 rearrangements 685s Finished SNPs 685s Finished ref gaps 685s Finished read gaps 685s Mutating sequence Sim.pm.2 685s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 685s Finished SNPs 685s Finished ref gaps 685s Finished read gaps 685s Mutated reference genome to subject genome 685s SNPs introduced: 11 685s Reference gaps introduced: 0 685s Read gaps introduced: 3 685s Rearrangements introduced: 3 685s Created read sampler 685s Sampling 53 reads 685s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 685s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 685s parsing sequence Sim.pm.1... 685s parsing sequence Sim.pm.2... 685s Parsed 234 reference bases 685s *** Run 2 of 100 685s /usr/bin/bowtie2 -a --norc --trim5 3 --local --cp-ival 4 --trim3 2 --mp 4.95394998094335,3.96497903113403 --rfg 45.0832266821872,4.7880210997452 --cp-min 3 --large-index --score-min L,6.18106109806811,8.21843572685823 -R 1 -f -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta 685s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '21' because it was < 2 characters long 685s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '25' because it was < 2 characters long 685s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '26' because it was < 2 characters long 685s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 685s Warning: skipping read '27' because it was < 2 characters long 685s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '38' because it was < 2 characters long 685s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '40' because it was < 2 characters long 685s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 685s Warning: skipping read '41' because it was < 2 characters long 685s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '42' because it was < 2 characters long 685s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '47' because it was < 2 characters long 685s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 685s Warning: skipping read '49' because it was < 2 characters long 685s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '51' because it was < 2 characters long 685s 53 reads; of these: 685s 53 (100.00%) were unpaired; of these: 685s 53 (100.00%) aligned 0 times 685s 0 (0.00%) aligned exactly 1 time 685s 0 (0.00%) aligned >1 times 685s 0.00% overall alignment rate 685s Read 50 alignments... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s /usr/bin/bowtie2 -a --norc --trim5 3 --local --cp-ival 4 --trim3 2 --mp 4.95394998094335,3.96497903113403 --rfg 45.0832266821872,4.7880210997452 --cp-min 3 --large-index --score-min L,6.18106109806811,8.21843572685823 -R 1 -f -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 685s Processing line... 685s Processing line... 685s Processing line... 685s --- Summary --- 685s Read 1 reference strings 685s Checked 0 alignments, 0 edits 685s --------------- 685s PASSED 685s ALSO checking that bowtie2 and bowtie2-align match up 685s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '21' because it was < 2 characters long 685s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '25' because it was < 2 characters long 685s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '26' because it was < 2 characters long 685s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 685s Warning: skipping read '27' because it was < 2 characters long 685s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '38' because it was < 2 characters long 685s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '40' because it was < 2 characters long 685s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 685s Warning: skipping read '41' because it was < 2 characters long 685s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '42' because it was < 2 characters long 685s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '47' because it was < 2 characters long 685s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 685s Warning: skipping read '49' because it was < 2 characters long 685s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '51' because it was < 2 characters long 685s 53 reads; of these: 685s 53 (100.00%) were unpaired; of these: 685s 53 (100.00%) aligned 0 times 685s 0 (0.00%) aligned exactly 1 time 685s 0 (0.00%) aligned >1 times 685s 0.00% overall alignment rate 685s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 685s Flattened IUPAC characters 685s Mutating sequence Sim.pm.2 685s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 685s Finished SNPs 685s Finished ref gaps 685s Finished read gaps 685s Mutating sequence Sim.pm.1 685s Introducing 15 SNPs, 0/3 ref/read gaps, and 2 rearrangements 685s Finished SNPs 685s Finished ref gaps 685s Finished read gaps 685s Mutated reference genome to subject genome 685s SNPs introduced: 23 685s Reference gaps introduced: 1 685s Read gaps introduced: 3 685s Rearrangements introduced: 2 685s Created read sampler 685s Sampling 130 reads 685s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 685s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 685s parsing sequence Sim.pm.1... 685s parsing sequence Sim.pm.2... 685s Parsed 234 reference bases 685s *** Run 3 of 100 685s /usr/bin/bowtie2 --score-min L,5.40060146015656,7.7641411334984 --trim3 5 --ma 14.2684214416965 -k 2 -R 4 --rdg 2.56595289060194 --rfg 26.7228048841648 --mm --large-index --cp-min 2 --trim5 9 --cp-ival 3 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 685s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 685s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '1' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 685s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '4' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 685s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '6' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 685s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '10' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 685s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '13' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 685s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '17' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 685s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '22' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 685s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '23' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 685s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '26' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 685s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '31' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 685s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '36' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 685s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '45' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 685s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '47' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 685s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '49' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 685s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '52' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 685s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '55' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 685s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '57' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 685s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '59' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 685s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '63' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 685s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '66' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 685s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '72' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 685s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '75' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 685s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '76' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 685s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '77' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 685s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '84' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 685s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '85' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 685s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '86' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 685s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '88' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 685s Read 50 alignments... 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 685s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '93' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 685s Warning: skipping mate #2 of read '96' because length (1) <= # seed mismatches (0) 685s Warning: skipping mate #2 of read '96' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 685s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '98' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 685s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '99' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 685s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '100' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 685s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '103' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 685s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '105' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 685s Warning: skipping mate #2 of read '108' because length (1) <= # seed mismatches (0) 685s Warning: skipping mate #2 of read '108' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 685s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '110' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 685s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '112' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 685s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '114' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 685s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '115' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 685s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '117' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 685s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '118' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 685s Warning: skipping mate #1 of read '121' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '121' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 685s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '122' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 685s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '123' because it was < 2 characters long 685s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 685s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 685s Read 100 alignments... 685s Read 150 alignments... 685s Read 200 alignments... 685s 130 reads; of these: 685s 95 (73.08%) were paired; of these: 685s 93 (97.89%) aligned concordantly 0 times 685s 1 (1.05%) aligned concordantly exactly 1 time 685s 1 (1.05%) aligned concordantly >1 times 685s ---- 685s 93 pairs aligned concordantly 0 times; of these: 685s 1 (1.08%) aligned discordantly 1 time 685s ---- 685s 92 pairs aligned 0 times concordantly or discordantly; of these: 685s 184 mates make up the pairs; of these: 685s 163 (88.59%) aligned 0 times 685s 6 (3.26%) aligned exactly 1 time 685s 15 (8.15%) aligned >1 times 685s 35 (26.92%) were unpaired; of these: 685s 30 (85.71%) aligned 0 times 685s 2 (5.71%) aligned exactly 1 time 685s 3 (8.57%) aligned >1 times 685s 14.22% overall alignment rate 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GTTCGATTCGGTTGGTTTATGTCA 685s GTTCGATTCGGTTGGTTTATGTCA 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TGTCG 685s TGTCG 685s Processing line... 685s TGTCG 685s TGTCG 685s Processing line... 685s Processing line... 685s GTTG 685s GTTG 685s Processing line... 685s GTTG 685s GTTG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GTTCCCGGT 685s GTTCCCGGT 685s Processing line... 685s GTTCCCGGT 685s GTTCCCGGT 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TG 685s TG 685s Processing line... 685s TG 685s TG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GG 685s GG 685s Processing line... 685s GG 685s GG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s CGGGGCCAGTTCGA 685s CGGGGCCAGTTCGA 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GAC 685s GAC 685s Processing line... 685s GTC 685s GTC 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GGG 685s GGG 685s Processing line... 685s GGG 685s GGG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGA 685s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGA 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s CGGCGGGGCCAGTTCGATTCG 685s CGGCGGGGCCAGTTCGATTCG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TTCC 685s TTCC 685s Processing line... 685s TTCC 685s TTCC 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GGTTGGTTTATGTCATCGCGCGGTTGTTTGG 685s GGTTGGTTTATGTCATCGCGCGGTTGTTTGG 685s Processing line... 685s GGGGGTCTCAGGT 685s GGGGGTCTCAGGT 685s Processing line... 685s Processing line... 685s Processing line... 685s GGT 685s GGT 685s Processing line... 685s GGT 685s GGT 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GTTCC 685s GTTCC 685s Processing line... 685s GTTCC 685s GTTCC 685s Processing line... 685s TGGT 685s TGGT 685s Processing line... 685s TGGT 685s TGGT 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TCGG 685s TCGG 685s Processing line... 685s GTTTATGTCATCGCGCGGTTGTTTGGTGTG 685s GTTTATGTCATCGCGCGGTTGTTTGGTGTG 685s Processing line... 685s GGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGC 685s GGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGC 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TCAGGTTGGAGTCCCGCGGCCCG 685s TCAGGTTGGAGTCCCGCGGCCCG 685s Processing line... 685s Processing line... 685s GTTCCCGGT 685s GTTCCCGGT 685s Processing line... 685s GTTCCCGGT 685s GTTCCCGGT 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TT 685s TT 685s Processing line... 685s TT 685s TT 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s CGCGC 685s CGCGC 685s Processing line... 685s GCGCG 685s GCGCG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GCGGCGGGGCCAGTTCGATTCGGTTGGTTTATG 685s GCGGCGGGGCCAGTTCGATTCGGTTGGTTTATG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TTTGGT 685s TTTGGT 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GGG 685s GGG 685s Processing line... 685s TCG 685s TCG 685s Processing line... 685s GGG 685s GGG 685s Processing line... 685s TCG 685s TCG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TTGG 685s TTGG 685s Processing line... 685s TTGG 685s TTGG 685s Processing line... 685s GCCGT 685s GCCGT 685s Processing line... 685s GCCGT 685s GCCGT 685s Processing line... 685s Processing line... 685s Processing line... 685s GCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 685s GCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 685s Processing line... 685s GCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 685s GCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TGCG 685s TGCG 685s Processing line... 685s TGCG 685s TGCG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s --- Summary --- 685s Read 1 reference strings 685s Checked 52 alignments, 0 edits 685s --------------- 685s PASSED 685s Flattened IUPAC characters 685s Mutating sequence Sim.pm.1 685s Introducing 1 SNPs, 1/1 ref/read gaps, and 3 rearrangements 685s Finished SNPs 685s Finished ref gaps 685s Finished read gaps 685s Mutating sequence Sim.pm.2 685s Introducing 7 SNPs, 3/0 ref/read gaps, and 1 rearrangements 685s Finished SNPs 685s Finished ref gaps 685s Finished read gaps 685s Mutated reference genome to subject genome 685s SNPs introduced: 8 685s Reference gaps introduced: 4 685s Read gaps introduced: 1 685s Rearrangements introduced: 4 685s Created read sampler 685s Sampling 91 reads 685s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 685s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 685s parsing sequence Sim.pm.1... 685s parsing sequence Sim.pm.2... 685s Parsed 234 reference bases 685s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '1' because it was < 2 characters long 685s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '21' because it was < 2 characters long 685s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '23' because it was < 2 characters long 685s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 685s Warning: skipping mate #2 of read '32' because it was < 2 characters long 685s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '33' because it was < 2 characters long 685s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '35' because it was < 2 characters long 685s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '39' because it was < 2 characters long 685s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '43' because it was < 2 characters long 685s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '47' because it was < 2 characters long 685s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '48' because it was < 2 characters long 685s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '52' because it was < 2 characters long 685s Warning: skipping mate #2 of read '52' because it was < 2 characters long 685s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '53' because it was < 2 characters long 685s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 685s Warning: skipping mate #2 of read '54' because it was < 2 characters long 685s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '55' because it was < 2 characters long 685s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 685s Warning: skipping read '60' because it was < 2 characters long 685s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '64' because it was < 2 characters long 685s Warning: skipping mate #2 of read '68' because length (1) <= # seed mismatches (0) 685s Warning: skipping mate #2 of read '68' because it was < 2 characters long 685s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '74' because it was < 2 characters long 685s Read 50 alignments... 685s Read 100 alignments... 685s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '79' because it was < 2 characters long 685s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 685s Warning: skipping mate #1 of read '86' because it was < 2 characters long 685s 91 reads; of these: 685s 78 (85.71%) were paired; of these: 685s 78 (100.00%) aligned concordantly 0 times 685s 0 (0.00%) aligned concordantly exactly 1 time 685s 0 (0.00%) aligned concordantly >1 times 685s ---- 685s 78 pairs aligned concordantly 0 times; of these: 685s 0 (0.00%) aligned discordantly 1 time 685s ---- 685s 78 pairs aligned 0 times concordantly or discordantly; of these: 685s 156 mates make up the pairs; of these: 685s 125 (80.13%) aligned 0 times 685s 24 (15.38%) aligned exactly 1 time 685s 7 (4.49%) aligned >1 times 685s 13 (14.29%) were unpaired; of these: 685s 13 (100.00%) aligned 0 times 685s 0 (0.00%) aligned exactly 1 time 685s 0 (0.00%) aligned >1 times 685s 18.34% overall alignment rate 685s Read 150 alignments... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GGGGGCGTGGGTTCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGGCTG--G 685s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GCGGCGGGGCCAGTTCGATTCGGTTGGTCTATGTCATCGCGCGGTTGT 685s GCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGT 685s *** Run 4 of 100 685s /usr/bin/bowtie2 --rdg 6.75349087596253 --mm --score-min L,5.68582048699946,1.07082081493911 -R 2 -k 2 --np 1 --cp-min 7 --large-index --nofw --trim3 7 --local --cp-ival 2 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GTTCCCGGTG 685s GTTCCCGGTG 685s Processing line... 685s GTTCCCGGTG 685s GTTCCCGGTG 685s Processing line... 685s Processing line... 685s TTCGATTCGGTTGGTCTATGTCATCGCGCGGTTGTTTGGTGT 685s TTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGT 685s Processing line... 685s Processing line... 685s Processing line... 685s TGACGCCGTTGAACGTGCG 685s TGACGCCGTTGAACGTGCG 685s Processing line... 685s Processing line... 685s TGGTCTATGTCATCGCGCGGTTGT 685s TGGTTTATGTCATCGCGCGGTTGT 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GGGCGTGGGTTCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTT 685s GGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTT 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s CGGGGCC 685s CGGGGCC 685s Processing line... 685s CGGGGCC 685s CGGGGCC 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAG 685s GGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNG---G 685s Processing line... 685s Processing line... 685s Processing line... 685s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGG 685s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TTGTAGGCCGTTG 685s TTGTAGGCCGTTG 685s Processing line... 685s TTGTAGGCCGTTG 685s TTGTAGGCCGTTG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GCCAGTTCGATTCGG 685s GCCAGTTCGATTCGG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TAGGTAGCGGGCTGGTGACGCCGTTGAACGTGCGGCGGGG-C 685s TNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCGGCGGGGCC 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTCTATGTCATCGCGCGGTTGTTTGGTGTGTACGGGTGTCTCAGGTTCCAGGAGTCCCGCGGCCCGTTCGGTAGCGCGTCTGGTGACGCCGTTGATCGTGC-G 685s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTT---GGAGTCCCGCGGCCCGTTNGGTAGCG-GNCTGGTGACGCCGTTGAACGTGCGG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTCTATGTCATCGCGCGG 685s GGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGG 685s Processing line... 685s Processing line... 685s Processing line... 685s GAGTCCCGCGGCCCGTTAGGTAGCGGGCTGGTGACGCCGTTGAACGTGCGGCGGGGCCAGTTCG 685s GAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCGGCGGGGCCA----G 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GTTTATGTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGG---------GCTG 685s GTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s CGGCGGGGCCAGTTCGATTCGGTTGGTCTATGTCATCGCGCGGTTGTTTGGTG 685s CGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTG--G 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TGTTCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGGCTGGTGACGCCGTTGAACGTGCGGCGG 685s TGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCGGC-G 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GGTCTCAGGTTGGAGTCCC 685s GGTCTCAGGTTGGAGTCCC 685s Processing line... 685s Processing line... 685s TGTCATCGCGCGGTTGTTTGGTGTGTTC-GG 685s TGTCATCGCGCGGTTGTTTGGTGTGTNCGGG 685s Processing line... 685s Processing line... 685s GGGGGCGTGGGTTCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGT 685s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGT 685s Processing line... 685s Processing line... 685s CGATTCGGTTGGTCTATGTCATCGCGCGGTTGTTTGGTGTGTACGGG 685s CGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNC-GG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTG 685s TGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTG 685s Processing line... 685s TGTCGTTGTAGGCCGTTGGGGTTC 685s TGTCGTTGTAGGCCGTTGGGGTTC 685s Processing line... 685s Processing line... 685s GGGGGCGTGGGTTCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGGCTGGTGACGCCGTTGAACGTGC-G 685s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCGG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s TCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTT 685s TCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTT 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GTTGTTTGGT 685s GTTGTTTGGT 685s Processing line... 685s Processing line... 685s Processing line... 685s CGCCGTTCCCGGTGTGTCGTTGTAG 685s CGCCGTTCCCGGTGTGTCGTTGTAG 685s Processing line... 685s CGCCGTTCCCGGTGTGTCGTTGTAG 685s CGCCGTTCCCGGTGTGTCGTTGTAG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GTTGGGGTTCGCCGTTCCCGGTGTGT 685s GTTGGGGTTCGCCGTTCCCGGTGTGT 685s Processing line... 685s GTTGGGGTTCGCCGTTCCCGGTGTGT 685s GTTGGGGTTCGCCGTTCCCGGTGTGT 685s Processing line... 685s Processing line... 685s GGGGCCAGTTCGATTCGGTTGG 685s GGGGCCAGTTCGATTCGGTTGG 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s Processing line... 685s GGTTCGCCGTTCC 685s GGTTCGCCGTTCC 685s Processing line... 685s GGTTCGCCGTTCC 685s GGTTCGCCGTTCC 685s Processing line... 685s --- Summary --- 685s Read 1 reference strings 685s Checked 38 alignments, 0 edits 685s --------------- 685s PASSED 685s Flattened IUPAC characters 685s Mutating sequence Sim.pm.2 685s Introducing 17 SNPs, 1/2 ref/read gaps, and 1 rearrangements 685s Finished SNPs 685s Finished ref gaps 685s Finished read gaps 685s Mutating sequence Sim.pm.1 685s Introducing 7 SNPs, 2/0 ref/read gaps, and 1 rearrangements 685s Finished SNPs 685s *** Run 5 of 100 685s /usr/bin/bowtie2 --n-ceil 0.659190965598092,0.282900011188584 --trim5 5 --norc --cp-ival 6 --mp 1.78931737369484,1.4850824690573 --trim3 8 --rfg 8.92037252394094 --np 3 --cp-min 6 --large-index -R 2 -k 2 --gbar 14 --score-min L,5.71982138100305,6.46552804604633 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq 685s Finished ref gaps 685s Finished read gaps 685s Mutated reference genome to subject genome 685s SNPs introduced: 24 685s Reference gaps introduced: 3 685s Read gaps introduced: 2 685s Rearrangements introduced: 2 685s Created read sampler 685s Sampling 232 reads 685s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 685s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 685s parsing sequence Sim.pm.1... 685s parsing sequence Sim.pm.2... 685s Parsed 234 reference bases 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 686s Warning: skipping mate #2 of read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 686s Warning: skipping mate #2 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 686s Read 50 alignments... 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 686s Warning: skipping mate #2 of read 'R_1_1_1_123_123_1/1' because length (1) <= # seed mismatches (0) 686s Warning: skipping mate #2 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_143_143_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_143_143_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 686s Read 100 alignments... 686s Read 150 alignments... 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_145_145_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_151_151_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_153_153_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_153_153_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_155_155_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_155_155_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_158_158_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_159_159_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_160_160_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_160_160_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_160_160_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 686s Read 200 alignments... 686s Read 250 alignments... 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_162_162_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_163_163_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_164_164_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_165_165_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_165_165_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_166_166_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_166_166_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_169_169_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_169_169_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_172_172_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_172_172_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_176_176_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_179_179_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_179_179_1/1' because length (1) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_179_179_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_181_181_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_182_182_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_182_182_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_183_183_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_183_183_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_183_183_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_183_183_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_184_184_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_184_184_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_185_185_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_185_185_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_185_185_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_186_186_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_186_186_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_187_187_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_187_187_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_187_187_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_188_188_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_188_188_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_189_189_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_189_189_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_189_189_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_189_189_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_190_190_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_190_190_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_190_190_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_190_190_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_191_191_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_191_191_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_192_192_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_192_192_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_193_193_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_193_193_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_193_193_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_194_194_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_194_194_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_195_195_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_195_195_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_196_196_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_197_197_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_197_197_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_198_198_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_198_198_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_198_198_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_199_199_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_199_199_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_199_199_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_199_199_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_200_200_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_200_200_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_201_201_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_201_201_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_201_201_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_201_201_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_202_202_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_202_202_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_202_202_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_202_202_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_203_203_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_203_203_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_203_203_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_203_203_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_204_204_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_204_204_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_205_205_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_205_205_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_206_206_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_207_207_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_207_207_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_208_208_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_208_208_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_208_208_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_208_208_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_209_209_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_209_209_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_210_210_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_211_211_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_212_212_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_212_212_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_213_213_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_214_214_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_214_214_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_214_214_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_214_214_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_215_215_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_216_216_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_217_217_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_217_217_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_218_218_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_219_219_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_219_219_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_220_220_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_220_220_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_221_221_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_221_221_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_222_222_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_222_222_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_222_222_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_223_223_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_223_223_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_223_223_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_223_223_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_224_224_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_224_224_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_224_224_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_224_224_1/1' because it was < 2 characters long 686s Read 300 alignments... 686s Read 350 alignments... 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_225_225_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_225_225_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_225_225_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_225_225_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_226_226_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_227_227_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_227_227_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_228_228_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_228_228_1/1; setting to 0 instead 686s Warning: skipping mate #1 of read 'R_1_1_1_228_228_1/1' because length (1) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read 'R_1_1_1_228_228_1/1' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_229_229_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_229_229_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_230_230_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_230_230_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_231_231_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_231_231_1/1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_232_232_1/1; setting to 0 instead 686s Warning: skipping read 'R_1_1_1_232_232_1/1' because length (0) <= # seed mismatches (0) 686s Warning: skipping read 'R_1_1_1_232_232_1/1' because it was < 2 characters long 686s 232 reads; of these: 686s 172 (74.14%) were paired; of these: 686s 170 (98.84%) aligned concordantly 0 times 686s 0 (0.00%) aligned concordantly exactly 1 time 686s 2 (1.16%) aligned concordantly >1 times 686s ---- 686s 170 pairs aligned concordantly 0 times; of these: 686s 0 (0.00%) aligned discordantly 1 time 686s ---- 686s 170 pairs aligned 0 times concordantly or discordantly; of these: 686s 340 mates make up the pairs; of these: 686s 314 (92.35%) aligned 0 times 686s 7 (2.06%) aligned exactly 1 time 686s 19 (5.59%) aligned >1 times 686s 60 (25.86%) were unpaired; of these: 686s 58 (96.67%) aligned 0 times 686s 1 (1.67%) aligned exactly 1 time 686s 1 (1.67%) aligned >1 times 686s 7.92% overall alignment rate 686s Read 400 alignments... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GGCGTGGGTGCGGCGGGGC 686s GGCGTGGGTGCGGCGGGGC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s AGGCCGTTGGG 686s AGGCCGTTGGG 686s Processing line... 686s AGGCCGTTGGG 686s AGGCCGTTGGG 686s Processing line... 686s CCA 686s CCA 686s Processing line... 686s CCA 686s CCA 686s Processing line... 686s GGGGT 686s GGGGT 686s Processing line... 686s GGGGT 686s GGGGT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TGGTGACGC 686s TGGTGACGC 686s Processing line... 686s ACG 686s ACG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CG 686s CG 686s Processing line... 686s CG 686s CG 686s Processing line... 686s Processing line... 686s GGGTTCGCCGTTCCCGG 686s GGGTTCGCCGTTCCCGG 686s Processing line... 686s GGGTTCGCCGTTCCCGG 686s GGGTTCGCCGTTCCCGG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GCCGTTG 686s GCCGTTG 686s Processing line... 686s GCCGTTG 686s GCCGTTG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GTTCGCC 686s GTTCGCC 686s Processing line... 686s GTTCGCC 686s GTTCGCC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CCCGT 686s CCCGT 686s Processing line... 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TGTC 686s TGTC 686s Processing line... 686s TGTC 686s TGTC 686s Processing line... 686s Processing line... 686s GTGGGTGCGGCG 686s GTGGGTGCGGCG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CAG 686s CAG 686s Processing line... 686s CAG 686s CAG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CA 686s CA 686s Processing line... 686s CA 686s CA 686s Processing line... 686s Processing line... 686s TG 686s TG 686s Processing line... 686s TG 686s TG 686s Processing line... 686s GCGTGGGTGCGGCGGGGCCA 686s GCGTGGGTGCGGCGGGGCCA 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GTA 686s GTA 686s Processing line... 686s GTA 686s GTA 686s Processing line... 686s Processing line... 686s TT 686s TT 686s Processing line... 686s TT 686s TT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GGTGC 686s GGTGC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CCCG 686s CCCG 686s Processing line... 686s GGCGGGG 686s GGCGGGG 686s Processing line... 686s CCCG 686s CCCG 686s Processing line... 686s GGCGGGG 686s GGCGGGG 686s Processing line... 686s Processing line... 686s GGTG 686s GGTG 686s Processing line... 686s GGTG 686s GGTG 686s Processing line... 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GAC 686s GAC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TTGTTTG 686s TTGTTTG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s AGGCCG 686s AGGCCG 686s Processing line... 686s AGGCCG 686s AGGCCG 686s *** Run 6 of 100 686s /usr/bin/bowtie2 --cp-ival 2 --local --trim5 3 --cp-min 3 -M 4 --large-index --rfg 4.22896743540756,14.8836238077413 -D 23 --trim3 2 --score-min L,9.04612552603738,7.03320299686038 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s AC 686s AC 686s Processing line... 686s AC 686s AC 686s Processing line... 686s TTCGGTT 686s TTCGGTT 686s Processing line... 686s Processing line... 686s Processing line... 686s GCG 686s GCG 686s Processing line... 686s GCG 686s GCG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s --- Summary --- 686s Read 1 reference strings 686s Checked 54 alignments, 0 edits 686s --------------- 686s PASSED 686s Flattened IUPAC characters 686s Mutating sequence Sim.pm.2 686s Introducing 18 SNPs, 2/1 ref/read gaps, and 0 rearrangements 686s Finished SNPs 686s Finished ref gaps 686s Finished read gaps 686s Mutating sequence Sim.pm.1 686s Introducing 16 SNPs, 0/0 ref/read gaps, and 1 rearrangements 686s Finished SNPs 686s Finished ref gaps 686s Finished read gaps 686s Mutated reference genome to subject genome 686s SNPs introduced: 34 686s Reference gaps introduced: 2 686s Read gaps introduced: 1 686s Rearrangements introduced: 1 686s Created read sampler 686s Sampling 68 reads 686s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 686s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 686s parsing sequence Sim.pm.1... 686s parsing sequence Sim.pm.2... 686s Parsed 234 reference bases 686s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 686s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '11' because it was < 2 characters long 686s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '15' because it was < 2 characters long 686s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '19' because it was < 2 characters long 686s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 686s Warning: skipping read '25' because it was < 2 characters long 686s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '27' because it was < 2 characters long 686s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '28' because it was < 2 characters long 686s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '34' because it was < 2 characters long 686s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '39' because it was < 2 characters long 686s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '43' because it was < 2 characters long 686s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '49' because it was < 2 characters long 686s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '55' because it was < 2 characters long 686s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '59' because it was < 2 characters long 686s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '66' because it was < 2 characters long 686s 68 reads; of these: 686s 68 (100.00%) were unpaired; of these: 686s 68 (100.00%) aligned 0 times 686s 0 (0.00%) aligned exactly 1 time 686s 0 (0.00%) aligned >1 times 686s 0.00% overall alignment rate 686s Read 50 alignments... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s --- Summary --- 686s Read 1 reference strings 686s Checked 0 alignments, 0 edits 686s --------------- 686s PASSED 686s ALSO checking that bowtie2 and bowtie2-align match up 686s /usr/bin/bowtie2 --cp-ival 2 --local --trim5 3 --cp-min 3 -M 4 --large-index --rfg 4.22896743540756,14.8836238077413 -D 23 --trim3 2 --score-min L,9.04612552603738,7.03320299686038 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 686s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 686s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '11' because it was < 2 characters long 686s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '15' because it was < 2 characters long 686s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '19' because it was < 2 characters long 686s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 686s Warning: skipping read '25' because it was < 2 characters long 686s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '27' because it was < 2 characters long 686s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '28' because it was < 2 characters long 686s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '34' because it was < 2 characters long 686s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '39' because it was < 2 characters long 686s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '43' because it was < 2 characters long 686s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '49' because it was < 2 characters long 686s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '55' because it was < 2 characters long 686s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '59' because it was < 2 characters long 686s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '66' because it was < 2 characters long 686s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 686s 68 reads; of these: 686s 68 (100.00%) were unpaired; of these: 686s 68 (100.00%) aligned 0 times 686s 0 (0.00%) aligned exactly 1 time 686s 0 (0.00%) aligned >1 times 686s 0.00% overall alignment rate 686s Flattened IUPAC characters 686s Mutating sequence Sim.pm.2 686s Introducing 10 SNPs, 0/1 ref/read gaps, and 0 rearrangements 686s Finished SNPs 686s Finished ref gaps 686s Finished read gaps 686s Mutating sequence Sim.pm.1 686s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 686s Finished SNPs 686s Finished ref gaps 686s Finished read gaps 686s Mutated reference genome to subject genome 686s SNPs introduced: 18 686s Reference gaps introduced: 1 686s Read gaps introduced: 1 686s Rearrangements introduced: 0 686s Created read sampler 686s Sampling 79 reads 686s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 686s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 686s parsing sequence Sim.pm.1... 686s *** Run 7 of 100 686s /usr/bin/bowtie2 --cp-min 2 --large-index --trim5 0 --local --cp-ival 3 --trim3 4 --score-min L,7.74800092753958,9.2647379452841 --rdg 40.7314017909435 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 686s parsing sequence Sim.pm.2... 686s Parsed 234 reference bases 686s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '2' because it was < 2 characters long 686s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '7' because it was < 2 characters long 686s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '15' because it was < 2 characters long 686s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '29' because it was < 2 characters long 686s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '33' because it was < 2 characters long 686s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '44' because it was < 2 characters long 686s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '49' because it was < 2 characters long 686s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '53' because it was < 2 characters long 686s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 686s Warning: skipping read '56' because it was < 2 characters long 686s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '65' because it was < 2 characters long 686s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '68' because it was < 2 characters long 686s 79 reads; of these: 686s 79 (100.00%) were unpaired; of these: 686s 79 (100.00%) aligned 0 times 686s 0 (0.00%) aligned exactly 1 time 686s 0 (0.00%) aligned >1 times 686s 0.00% overall alignment rate 686s Read 50 alignments... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s --- Summary --- 686s Read 1 reference strings 686s Checked 0 alignments, 0 edits 686s --------------- 686s PASSED 686s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 686s /usr/bin/bowtie2 --cp-min 2 --large-index --trim5 0 --local --cp-ival 3 --trim3 4 --score-min L,7.74800092753958,9.2647379452841 --rdg 40.7314017909435 -q -p 2 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 686s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '2' because it was < 2 characters long 686s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '7' because it was < 2 characters long 686s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '15' because it was < 2 characters long 686s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '29' because it was < 2 characters long 686s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '33' because it was < 2 characters long 686s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '44' because it was < 2 characters long 686s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '49' because it was < 2 characters long 686s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '53' because it was < 2 characters long 686s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 686s Warning: skipping read '56' because it was < 2 characters long 686s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '65' because it was < 2 characters long 686s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '68' because it was < 2 characters long 686s 79 reads; of these: 686s 79 (100.00%) were unpaired; of these: 686s 79 (100.00%) aligned 0 times 686s 0 (0.00%) aligned exactly 1 time 686s 0 (0.00%) aligned >1 times 686s 0.00% overall alignment rate 686s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 686s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 686s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 686s /usr/bin/bowtie2 --cp-min 2 --large-index --trim5 0 --local --cp-ival 3 --trim3 4 --score-min L,7.74800092753958,9.2647379452841 --rdg 40.7314017909435 -q -p 3 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 686s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 686s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '2' because it was < 2 characters long 686s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '7' because it was < 2 characters long 686s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '15' because it was < 2 characters long 686s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '29' because it was < 2 characters long 686s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '33' because it was < 2 characters long 686s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '44' because it was < 2 characters long 686s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '49' because it was < 2 characters long 686s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '53' because it was < 2 characters long 686s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 686s Warning: skipping read '56' because it was < 2 characters long 686s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '65' because it was < 2 characters long 686s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '68' because it was < 2 characters long 686s 79 reads; of these: 686s 79 (100.00%) were unpaired; of these: 686s 79 (100.00%) aligned 0 times 686s 0 (0.00%) aligned exactly 1 time 686s 0 (0.00%) aligned >1 times 686s 0.00% overall alignment rate 686s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 686s Flattened IUPAC characters 686s Mutating sequence Sim.pm.1 686s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 686s Finished SNPs 686s Finished ref gaps 686s Finished read gaps 686s Mutating sequence Sim.pm.2 686s Introducing 0 SNPs, 1/0 ref/read gaps, and 2 rearrangements 686s Finished SNPs 686s Finished ref gaps 686s Finished read gaps 686s Mutated reference genome to subject genome 686s SNPs introduced: 0 686s Reference gaps introduced: 1 686s Read gaps introduced: 0 686s Rearrangements introduced: 2 686s Created read sampler 686s Sampling 68 reads 686s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 686s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 686s parsing sequence Sim.pm.1... 686s parsing sequence Sim.pm.2... 686s Parsed 234 reference bases 686s *** Run 8 of 100 686s /usr/bin/bowtie2 --cp-min 2 --large-index --rdg 1.09747029109158 --mm --ma 35.8496675226939 --score-min L,1.79559518472552,1.70097716924877 --cp-ival 2 -a --trim5 3 --rfg 39.1442394388189 --trim3 2 -i C,3.35295573342649 -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta 686s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 686s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read '9' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 686s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read '15' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 686s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read '17' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 686s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read '21' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 686s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read '34' because it was < 2 characters long 686s Warning: skipping mate #2 of read '34' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 686s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 686s Warning: skipping mate #2 of read '36' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 686s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 686s Warning: skipping mate #2 of read '37' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 686s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read '38' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 686s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read '39' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 686s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read '41' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 686s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read '46' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 686s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 686s Warning: skipping mate #2 of read '51' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 686s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 686s Warning: skipping mate #2 of read '52' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 686s Read 50 alignments... 686s Read 100 alignments... 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 686s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 686s Warning: skipping mate #1 of read '67' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 686s 68 reads; of these: 686s 65 (95.59%) were paired; of these: 686s 64 (98.46%) aligned concordantly 0 times 686s 0 (0.00%) aligned concordantly exactly 1 time 686s 1 (1.54%) aligned concordantly >1 times 686s ---- 686s 64 pairs aligned concordantly 0 times; of these: 686s 1 (1.56%) aligned discordantly 1 time 686s ---- 686s 63 pairs aligned 0 times concordantly or discordantly; of these: 686s 126 mates make up the pairs; of these: 686s 94 (74.60%) aligned 0 times 686s 15 (11.90%) aligned exactly 1 time 686s 17 (13.49%) aligned >1 times 686s 3 (4.41%) were unpaired; of these: 686s 3 (100.00%) aligned 0 times 686s 0 (0.00%) aligned exactly 1 time 686s 0 (0.00%) aligned >1 times 686s 27.07% overall alignment rate 686s Read 150 alignments... 686s Read 200 alignments... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CGTG 686s CGTG 686s Processing line... 686s CGTG 686s CGTG 686s Processing line... 686s Processing line... 686s CGGTGTGTCGTTGTAGGCCGT 686s CGGTGTGTCGTTGTAGGCCGT 686s Processing line... 686s CGGTGTGTCGTTGTAGGCCGT 686s CGGTGTGTCGTTGTAGGCCGT 686s Processing line... 686s Processing line... 686s TGGA 686s TGGA 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CGCGGTTG 686s CGCGGTTG 686s Processing line... 686s GGTTGGTTTATGTCAT 686s GGTTGGTTTATGTCAT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GGGGCCAGTTCGAT 686s GGGGCCAGTTCGAT 686s Processing line... 686s Processing line... 686s CCGG 686s CCGG 686s Processing line... 686s CCGG 686s CCGG 686s Processing line... 686s CCGG 686s CCGG 686s Processing line... 686s CCGG 686s CCGG 686s Processing line... 686s Processing line... 686s GTTGGAGTCCCGCGGCC 686s GTTGGAGTCCCGCGGCC 686s Processing line... 686s Processing line... 686s AGG 686s AGG 686s Processing line... 686s CCT 686s CCT 686s Processing line... 686s AGG 686s AGG 686s Processing line... 686s AGG 686s AGG 686s Processing line... 686s Processing line... 686s GTTGTAGGCC 686s GTTGTAGGCC 686s Processing line... 686s GTTGTAGGCC 686s GTTGTAGGCC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TTCCCGGTGTGTC 686s TTCCCGGTGTGTC 686s Processing line... 686s TTCCCGGTGTGTC 686s TTCCCGGTGTGTC 686s Processing line... 686s Processing line... 686s GTTGAACGTGCGGCGGGGCCA 686s GTTGAACGTGCGGCGGGGCCA 686s Processing line... 686s Processing line... 686s TGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTG 686s TGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTG 686s Processing line... 686s Processing line... 686s TCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCG 686s TCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TTCGATTC 686s TTCGATTC 686s Processing line... 686s CCGTTG 686s CCGTTG 686s Processing line... 686s CCGTTG 686s CCGTTG 686s Processing line... 686s CCGTTG 686s CCGTTG 686s Processing line... 686s Processing line... 686s Processing line... 686s GGGC 686s GGGC 686s Processing line... 686s GGGC 686s GGGC 686s Processing line... 686s GCCC 686s GCCC 686s Processing line... 686s GGGC 686s GGGC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GGGGCCA 686s GGGGCCA 686s Processing line... 686s GGGGCCA 686s GGGGCCA 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CCC 686s CCC 686s Processing line... 686s GCCAGTTCGATT 686s GCCAGTTCGATT 686s Processing line... 686s CCC 686s CCC 686s Processing line... 686s GCCAGTTCGATT 686s GCCAGTTCGATT 686s Processing line... 686s Processing line... 686s Processing line... 686s GTTTATGTCATCGCG 686s GTTTATGTCATCGCG 686s Processing line... 686s Processing line... 686s TTCGCCGTTCC 686s TTCGCCGTTCC 686s Processing line... 686s TTCGCCGTTCC 686s TTCGCCGTTCC 686s Processing line... 686s Processing line... 686s GGTCTCAGGTTGGAG 686s GGTCTCAGGTTGGAG 686s Processing line... 686s Processing line... 686s GTGTGTCGTTGTAGGCCGTTGG 686s GTGTGTCGTTGTAGGCCGTTGG 686s Processing line... 686s GTGTGTCGTTGTAGGCCGTTGG 686s GTGTGTCGTTGTAGGCCGTTGG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TCAGGTTGGAGT 686s TCAGGTTGGAGT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TTGGGGTTCGCCGTTCCCGGTG 686s TTGGGGTTCGCCGTTCCCGGTG 686s Processing line... 686s TTGGGGTTCGCCGTTCCCGGTG 686s TTGGGGTTCGCCGTTCCCGGTG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GTCAT 686s GTCAT 686s Processing line... 686s Processing line... 686s TTCGCCGTTCCCGGTGTGTCG 686s TTCGCCGTTCCCGGTGTGTCG 686s Processing line... 686s TTCGCCGTTCCCGGTGTGTCG 686s TTCGCCGTTCCCGGTGTGTCG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CC 686s CC 686s Processing line... 686s CC 686s CC 686s Processing line... 686s CC 686s CC 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s CC 686s CC 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s CC 686s CC 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s CC 686s CC 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s CC 686s CC 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s CC 686s CC 686s Processing line... 686s GG 686s GG 686s Processing line... 686s CC 686s CC 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s CC 686s CC 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s CC 686s CC 686s Processing line... 686s CC 686s CC 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s CC 686s CC 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s CC 686s CC 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s GG 686s GG 686s Processing line... 686s CC 686s CC 686s Processing line... 686s CC 686s CC 686s Processing line... 686s CC 686s CC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CCAGTTCGAT 686s CCAGTTCGAT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 686s TGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 686s Processing line... 686s TGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 686s TGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CGT 686s CGT 686s Processing line... 686s ACG 686s ACG 686s Processing line... 686s ACG 686s ACG 686s Processing line... 686s CGT 686s CGT 686s Processing line... 686s CGT 686s CGT 686s Processing line... 686s CGT 686s CGT 686s Processing line... 686s CGT 686s CGT 686s Processing line... 686s CGT 686s CGT 686s Processing line... 686s CGT 686s CGT 686s Processing line... 686s CGT 686s CGT 686s Processing line... 686s CGT 686s CGT 686s Processing line... 686s CGT 686s CGT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GTTTATGTCATCGCGCGGTT 686s GTTTATGTCATCGCGCGGTT 686s Processing line... 686s Processing line... 686s GCGGCGGGGCC 686s GCGGCGGGGCC 686s Processing line... 686s GCGGCGGGGCC 686s GCGGCGGGGCC 686s Processing line... 686s Processing line... 686s GACGCCGTTGAACGTGCGGCGGGG 686s GACGCCGTTGAACGTGCGGCGGGG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCC 686s TGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCC 686s Processing line... 686s --- Summary --- 686s Read 1 reference strings 686s Checked 128 alignments, 0 edits 686s --------------- 686s PASSED 686s Flattened IUPAC characters 686s Mutating sequence Sim.pm.1 686s Introducing 10 SNPs, 1/7 ref/read gaps, and 3 rearrangements 686s Finished SNPs 686s Finished ref gaps 686s Finished read gaps 686s Mutating sequence Sim.pm.2 686s Introducing 9 SNPs, 1/1 ref/read gaps, and 0 rearrangements 686s Finished SNPs 686s Finished ref gaps 686s Finished read gaps 686s Mutated reference genome to subject genome 686s SNPs introduced: 19 686s Reference gaps introduced: 2 686s Read gaps introduced: 8 686s Rearrangements introduced: 3 686s Created read sampler 686s Sampling 70 reads 686s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 686s *** Run 9 of 100 686s /usr/bin/bowtie2 --score-min L,1.73255939375029,8.54377088333505 --mm --cp-min 4 --large-index -N 1 -L21 --mp 5.15354777968096,4.96581530715074 --trim3 9 --rfg 32.0082719236161,19.6950479224693 --trim5 3 -M 7 --cp-ival 2 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 686s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 686s parsing sequence Sim.pm.1... 686s parsing sequence Sim.pm.2... 686s Parsed 234 reference bases 686s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 686s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 686s Warning: skipping read '0' because length (0) <= # seed mismatches (1) 686s Warning: skipping read '0' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 686s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 686s Warning: skipping read '4' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 686s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '9' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 686s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '10' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 686s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '12' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 686s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '19' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 686s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '22' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 686s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '28' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 686s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '30' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 686s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '31' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 686s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '35' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 686s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '37' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 686s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '43' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 686s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (1) 686s Warning: skipping mate #2 of read '47' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 686s Warning: skipping read '49' because length (1) <= # seed mismatches (1) 686s Warning: skipping read '49' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 686s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 686s Warning: skipping read '54' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 686s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 686s Warning: skipping read '57' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 686s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '62' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 686s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '64' because it was < 2 characters long 686s Read 50 alignments... 686s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 686s Read 100 alignments... 686s 70 reads; of these: 686s 56 (80.00%) were paired; of these: 686s 54 (96.43%) aligned concordantly 0 times 686s 0 (0.00%) aligned concordantly exactly 1 time 686s 2 (3.57%) aligned concordantly >1 times 686s ---- 686s 54 pairs aligned concordantly 0 times; of these: 686s 0 (0.00%) aligned discordantly 1 time 686s ---- 686s 54 pairs aligned 0 times concordantly or discordantly; of these: 686s 108 mates make up the pairs; of these: 686s 92 (85.19%) aligned 0 times 686s 6 (5.56%) aligned exactly 1 time 686s 10 (9.26%) aligned >1 times 686s 14 (20.00%) were unpaired; of these: 686s 12 (85.71%) aligned 0 times 686s 1 (7.14%) aligned exactly 1 time 686s 1 (7.14%) aligned >1 times 686s 17.46% overall alignment rate 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GTAG 686s GTAG 686s Processing line... 686s Processing line... 686s TGTTT 686s TGTTT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TCT 686s TCT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TGGGGTTC 686s TGGGGTTC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CGTTCCCGGTGTGT 686s CGTTCCCGGTGTGT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TGGAGTCCCGCGGCCCGT 686s TGGAGTCCCGCGGCCCGT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GGGCCAGTTCGATTCGGTTGGTT 686s GGGCCAGTTCGATTCGGTTGGTT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GG 686s GG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TAGGCCGTTGGGGTTCC 686s TAGGCCGTTGGGGTTCC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CCGTTCCCGGTGTGTCGTTGTA 686s CCGTTCCCGGTGTGTCGTTGTA 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TGTAG 686s TGTAG 686s Processing line... 686s Processing line... 686s CGCGCGGTTGTT 686s CGCGCGGTTGTT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GCCGTTCCCGGTGTGT 686s GCCGTTCCCGGTGTGT 686s Processing line... 686s Processing line... 686s Processing line... 686s GT 686s GT 686s Processing line... 686s CTCAGGTTGGAGTCCCGCGGCCC 686s CTCAGGTTGGAGTCCCGCGGCCC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GGGTTCGCCGTTCC 686s GGGTTCGCCGTTCC 686s Processing line... 686s TGCGG 686s TGCGG 686s Processing line... 686s CATCGCGCGGTTGTTT 686s CATCGCGCGGTTGTTT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s /usr/bin/bowtie2 --score-min L,1.73255939375029,8.54377088333505 --mm --cp-min 4 --large-index -N 1 -L21 --mp 5.15354777968096,4.96581530715074 --trim3 9 --rfg 32.0082719236161,19.6950479224693 --trim5 3 -M 7 --cp-ival 2 -r -p 4 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 686s TAGG 686s TAGG 686s Processing line... 686s CTGGTGACGCCGT 686s CTGGTGACGCCGT 686s Processing line... 686s Processing line... 686s GC 686s GC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s --- Summary --- 686s Read 1 reference strings 686s Checked 22 alignments, 0 edits 686s --------------- 686s PASSED 686s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 686s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 686s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 686s Warning: skipping read '0' because length (0) <= # seed mismatches (1) 686s Warning: skipping read '0' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 686s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 686s Warning: skipping read '4' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 686s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '9' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 686s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '10' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 686s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '12' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 686s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '19' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 686s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '22' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 686s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '28' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 686s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '30' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 686s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '31' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 686s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '35' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 686s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '37' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 686s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '43' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 686s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (1) 686s Warning: skipping mate #2 of read '47' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 686s Warning: skipping read '49' because length (1) <= # seed mismatches (1) 686s Warning: skipping read '49' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 686s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 686s Warning: skipping read '54' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 686s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 686s Warning: skipping read '57' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 686s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '62' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 686s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (1) 686s Warning: skipping mate #1 of read '64' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 686s 70 reads; of these: 686s 56 (80.00%) were paired; of these: 686s 54 (96.43%) aligned concordantly 0 times 686s 0 (0.00%) aligned concordantly exactly 1 time 686s 2 (3.57%) aligned concordantly >1 times 686s ---- 686s 54 pairs aligned concordantly 0 times; of these: 686s 0 (0.00%) aligned discordantly 1 time 686s ---- 686s 54 pairs aligned 0 times concordantly or discordantly; of these: 686s 108 mates make up the pairs; of these: 686s 92 (85.19%) aligned 0 times 686s 6 (5.56%) aligned exactly 1 time 686s 10 (9.26%) aligned >1 times 686s 14 (20.00%) were unpaired; of these: 686s 12 (85.71%) aligned 0 times 686s 1 (7.14%) aligned exactly 1 time 686s 1 (7.14%) aligned >1 times 686s 17.46% overall alignment rate 686s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 686s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 686s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 686s Flattened IUPAC characters 686s Mutating sequence Sim.pm.1 686s Introducing 9 SNPs, 3/2 ref/read gaps, and 1 rearrangements 686s Finished SNPs 686s Finished ref gaps 686s Finished read gaps 686s Mutating sequence Sim.pm.2 686s Introducing 10 SNPs, 2/0 ref/read gaps, and 2 rearrangements 686s Finished SNPs 686s Finished ref gaps 686s Finished read gaps 686s Mutated reference genome to subject genome 686s SNPs introduced: 19 686s Reference gaps introduced: 5 686s Read gaps introduced: 2 686s Rearrangements introduced: 3 686s Created read sampler 686s Sampling 77 reads 686s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 686s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 686s parsing sequence Sim.pm.1... 686s parsing sequence Sim.pm.2... 686s Parsed 234 reference bases 686s *** Run 10 of 100 686s /usr/bin/bowtie2 -N 0 -L16 --trim5 4 -a --cp-ival 2 -D 32 --score-min L,4.58907994631296,3.18425885013398 --rdg 44.1658472507713 --cp-min 3 --np 2 --large-index -f -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta 686s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 686s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '2' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 686s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '21' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 686s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '41' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 686s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '45' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 686s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 686s Warning: skipping read '47' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 686s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '48' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 686s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '49' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 686s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '59' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 686s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '60' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 686s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '64' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 686s Read 50 alignments... 686s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 686s Read 100 alignments... 686s 77 reads; of these: 686s 77 (100.00%) were unpaired; of these: 686s 60 (77.92%) aligned 0 times 686s 7 (9.09%) aligned exactly 1 time 686s 10 (12.99%) aligned >1 times 686s 22.08% overall alignment rate 686s Read 150 alignments... 686s Read 200 alignments... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TCGGTTGG 686s TCGGTTGG 686s Processing line... 686s Processing line... 686s Processing line... 686s GGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGT 686s GGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGT 686s Processing line... 686s GGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGT 686s GGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGT 686s Processing line... 686s TTGGGGTTCCCT 686s TTGGGGTTCCCT 686s Processing line... 686s Processing line... 686s Processing line... 686s CGGGGCCA 686s CGGGGCCA 686s Processing line... 686s CGGGGCCA 686s CGGGGCCA 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s TTC 686s TTC 686s Processing line... 686s GAA 686s GAA 686s Processing line... 686s TTC 686s TTC 686s Processing line... 686s TTC 686s TTC 686s Processing line... 686s TTC 686s TTC 686s Processing line... 686s TTC 686s TTC 686s Processing line... 686s TTC 686s TTC 686s Processing line... 686s TTC 686s TTC 686s Processing line... 686s CCGTTCCCGGTGTGTCGTTGTAG 686s CCGTTCCCGGTGTGTCGTTGTAG 686s Processing line... 686s CCGTTCCCGGTGTGTCGTTGTAG 686s CCGTTCCCGGTGTGTCGTTGTAG 686s Processing line... 686s Processing line... 686s Processing line... 686s AG 686s AG 686s Processing line... 686s CT 686s CT 686s Processing line... 686s AG 686s AG 686s Processing line... 686s CT 686s CT 686s Processing line... 686s AG 686s AG 686s Processing line... 686s CT 686s CT 686s Processing line... 686s AG 686s AG 686s Processing line... 686s AG 686s AG 686s Processing line... 686s AG 686s AG 686s Processing line... 686s AG 686s AG 686s Processing line... 686s Processing line... 686s Processing line... 686s GCG 686s GCG 686s Processing line... 686s CGC 686s CGC 686s Processing line... 686s GCG 686s GCG 686s Processing line... 686s CGC 686s CGC 686s Processing line... 686s CGC 686s CGC 686s Processing line... 686s CGC 686s CGC 686s Processing line... 686s GCG 686s GCG 686s Processing line... 686s CGC 686s CGC 686s Processing line... 686s GCG 686s GCG 686s Processing line... 686s GCG 686s GCG 686s Processing line... 686s GCG 686s GCG 686s Processing line... 686s GCG 686s GCG 686s Processing line... 686s GCG 686s GCG 686s Processing line... 686s GCG 686s GCG 686s Processing line... 686s CGC 686s CGC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s AC 686s AC 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s AC 686s AC 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s GT 686s GT 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s GGGGTCTC 686s GGGGTCTC 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CCG 686s CCG 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s CCG 686s CCG 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s CCG 686s CCG 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s CCG 686s CCG 686s Processing line... 686s CCG 686s CCG 686s Processing line... 686s CCG 686s CCG 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s CCG 686s CCG 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s CCG 686s CCG 686s Processing line... 686s CCG 686s CCG 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s CGG 686s CGG 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s Processing line... 686s CATCGC 686s CATCGC 686s Processing line... 686s GCGT 686s GCGT 686s Processing line... 686s ACGC 686s ACGC 686s Processing line... 686s Processing line... 686s TGGGTG 686s TGGGTG 686s Processing line... 686s Processing line... 686s Processing line... 686s CATCGC 686s CATCGC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s GC 686s GC 686s Processing line... 686s Processing line... 686s GGTTGGTT 686s GGTTGGTT 686s Processing line... 686s Processing line... 686s --- Summary --- 686s Read 1 reference strings 686s Checked 142 alignments, 0 edits 686s --------------- 686s PASSED 686s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 686s /usr/bin/bowtie2 -N 0 -L16 --trim5 4 -a --cp-ival 2 -D 32 --score-min L,4.58907994631296,3.18425885013398 --rdg 44.1658472507713 --cp-min 3 --np 2 --large-index -f -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 686s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 686s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '2' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 686s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '21' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 686s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '41' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 686s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '45' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 686s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 686s Warning: skipping read '47' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 686s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '48' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 686s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '49' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 686s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '59' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 686s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '60' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 686s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 686s Warning: skipping read '64' because it was < 2 characters long 686s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 686s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 686s 77 reads; of these: 686s 77 (100.00%) were unpaired; of these: 686s 60 (77.92%) aligned 0 times 686s 7 (9.09%) aligned exactly 1 time 686s 10 (12.99%) aligned >1 times 686s 22.08% overall alignment rate 686s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 687s Flattened IUPAC characters 687s Mutating sequence Sim.pm.1 687s Introducing 4 SNPs, 1/2 ref/read gaps, and 0 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutating sequence Sim.pm.2 687s Introducing 14 SNPs, 1/2 ref/read gaps, and 0 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutated reference genome to subject genome 687s SNPs introduced: 18 687s Reference gaps introduced: 2 687s Read gaps introduced: 4 687s Rearrangements introduced: 0 687s Created read sampler 687s Sampling 120 reads 687s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 687s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 687s parsing sequence Sim.pm.1... 687s *** Run 11 of 100 687s /usr/bin/bowtie2 --local --cp-ival 2 --cp-min 5 --large-index --n-ceil 1.25287677626802,0.99162038778315 --trim5 7 --rdg 28.3990077515671,6.55953066496184 --mm --score-min L,8.80476980489001,3.4027486379415 -R 3 --mp 9.50702184489782,2.287011359537 -f -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta 687s parsing sequence Sim.pm.2... 687s Parsed 234 reference bases 687s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '5' because it was < 2 characters long 687s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '27' because it was < 2 characters long 687s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '33' because it was < 2 characters long 687s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '42' because it was < 2 characters long 687s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '43' because it was < 2 characters long 687s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '44' because it was < 2 characters long 687s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '45' because it was < 2 characters long 687s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '50' because it was < 2 characters long 687s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '52' because it was < 2 characters long 687s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '57' because it was < 2 characters long 687s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '65' because it was < 2 characters long 687s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '69' because it was < 2 characters long 687s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '71' because it was < 2 characters long 687s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '74' because it was < 2 characters long 687s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '89' because it was < 2 characters long 687s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '95' because it was < 2 characters long 687s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '106' because it was < 2 characters long 687s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '113' because it was < 2 characters long 687s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '117' because it was < 2 characters long 687s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '118' because it was < 2 characters long 687s 120 reads; of these: 687s 120 (100.00%) were unpaired; of these: 687s 120 (100.00%) aligned 0 times 687s 0 (0.00%) aligned exactly 1 time 687s 0 (0.00%) aligned >1 times 687s 0.00% overall alignment rate 687s Read 50 alignments... 687s Read 100 alignments... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s /usr/bin/bowtie2 --local --cp-ival 2 --cp-min 5 --large-index --n-ceil 1.25287677626802,0.99162038778315 --trim5 7 --rdg 28.3990077515671,6.55953066496184 --mm --score-min L,8.80476980489001,3.4027486379415 -R 3 --mp 9.50702184489782,2.287011359537 -f -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s --- Summary --- 687s Read 1 reference strings 687s Checked 0 alignments, 0 edits 687s --------------- 687s PASSED 687s ALSO checking that bowtie2 and bowtie2-align match up 687s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '5' because it was < 2 characters long 687s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '27' because it was < 2 characters long 687s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '33' because it was < 2 characters long 687s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '42' because it was < 2 characters long 687s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '43' because it was < 2 characters long 687s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '44' because it was < 2 characters long 687s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '45' because it was < 2 characters long 687s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '50' because it was < 2 characters long 687s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '52' because it was < 2 characters long 687s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '57' because it was < 2 characters long 687s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '65' because it was < 2 characters long 687s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '69' because it was < 2 characters long 687s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '71' because it was < 2 characters long 687s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '74' because it was < 2 characters long 687s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '89' because it was < 2 characters long 687s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '95' because it was < 2 characters long 687s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '106' because it was < 2 characters long 687s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '113' because it was < 2 characters long 687s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '117' because it was < 2 characters long 687s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '118' because it was < 2 characters long 687s 120 reads; of these: 687s 120 (100.00%) were unpaired; of these: 687s 120 (100.00%) aligned 0 times 687s 0 (0.00%) aligned exactly 1 time 687s 0 (0.00%) aligned >1 times 687s 0.00% overall alignment rate 687s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 687s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 687s /usr/bin/bowtie2 --local --cp-ival 2 --cp-min 5 --large-index --n-ceil 1.25287677626802,0.99162038778315 --trim5 7 --rdg 28.3990077515671,6.55953066496184 --mm --score-min L,8.80476980489001,3.4027486379415 -R 3 --mp 9.50702184489782,2.287011359537 -f -p 3 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 687s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '5' because it was < 2 characters long 687s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '27' because it was < 2 characters long 687s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '33' because it was < 2 characters long 687s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '42' because it was < 2 characters long 687s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '43' because it was < 2 characters long 687s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '44' because it was < 2 characters long 687s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '45' because it was < 2 characters long 687s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '50' because it was < 2 characters long 687s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '52' because it was < 2 characters long 687s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '57' because it was < 2 characters long 687s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '65' because it was < 2 characters long 687s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '69' because it was < 2 characters long 687s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '71' because it was < 2 characters long 687s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '74' because it was < 2 characters long 687s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '89' because it was < 2 characters long 687s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '95' because it was < 2 characters long 687s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '106' because it was < 2 characters long 687s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '113' because it was < 2 characters long 687s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '117' because it was < 2 characters long 687s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '118' because it was < 2 characters long 687s 120 reads; of these: 687s 120 (100.00%) were unpaired; of these: 687s 120 (100.00%) aligned 0 times 687s 0 (0.00%) aligned exactly 1 time 687s 0 (0.00%) aligned >1 times 687s 0.00% overall alignment rate 687s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 687s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 687s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 687s Flattened IUPAC characters 687s Mutating sequence Sim.pm.2 687s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutating sequence Sim.pm.1 687s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutated reference genome to subject genome 687s SNPs introduced: 1 687s Reference gaps introduced: 0 687s Read gaps introduced: 2 687s Rearrangements introduced: 0 687s Created read sampler 687s Sampling 48 reads 687s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 687s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 687s parsing sequence Sim.pm.1... 687s parsing sequence Sim.pm.2... 687s Parsed 234 reference bases 687s *** Run 12 of 100 687s /usr/bin/bowtie2 --large-index --cp-min 2 -D 25 --score-min L,8.21337555914043,1.37461584147175 --mm --rdg 2.3907291466426 --n-ceil 0.0194931748122535,1.00789498010235 -M 5 --cp-ival 1 --local --mp 4.82402692690598,3.00796191751806 --trim3 8 --rfg 22.0186209085317,19.8692515543133 --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq 687s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 687s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 687s 48 reads; of these: 687s 48 (100.00%) were unpaired; of these: 687s 33 (68.75%) aligned 0 times 687s 12 (25.00%) aligned exactly 1 time 687s 3 (6.25%) aligned >1 times 687s 31.25% overall alignment rate 687s Read 50 alignments... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s TTCCCGGTGCGTCGTTGTAGGCCGTTGGGGTTCGCCG 687s TTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCG 687s Processing line... 687s Processing line... 687s TGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGT 687s TGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGT 687s Processing line... 687s GTCGTTGTAGGCCG 687s GTCGTTGTAGGCCG 687s Processing line... 687s GTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTGGTGACG-C 687s GTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCC 687s Processing line... 687s Processing line... 687s GTCGTTGTAGGCCGTTGGGGTTC 687s GTCGTTGTAGGCCGTTGGGGTTC 687s Processing line... 687s Processing line... 687s Processing line... 687s TGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCT--GG 687s TGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTG 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s TGGGTGCGGCGGGGCCAGTTCG 687s TGGGTGCGGCGGGGCCAGTTCG 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s TGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTG 687s TGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTG 687s Processing line... 687s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCC--TCGGTAGCGGGCTG 687s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTG 687s Processing line... 687s Processing line... 687s Processing line... 687s TTCGGTTGGTTTATGTCATCGCGC 687s TTCGGTTGGTTTATGTCATCGCGC 687s Processing line... 687s Processing line... 687s GGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGT------G 687s GGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGG 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s GTTTATGTCATC 687s GTTTATGTCATC 687s Processing line... 687s Processing line... 687s Processing line... 687s CAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCC--TCGGTAGCGGGCT--GG 687s CAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTG 687s Processing line... 687s Processing line... 687s GGCCAGTTCGATTCGGTTGGTTTATGTCA 687s GGCCAGTTCGATTCGGTTGGTTTATGTCA 687s Processing line... 687s GGTTTATGTCATCGCGCGGTTGTTTGGTGTGTAC-GGGG 687s GGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGG 687s /usr/bin/bowtie2 --large-index --cp-min 2 -D 25 --score-min L,8.21337555914043,1.37461584147175 --mm --rdg 2.3907291466426 --n-ceil 0.0194931748122535,1.00789498010235 -M 5 --cp-ival 1 --local --mp 4.82402692690598,3.00796191751806 --trim3 8 --rfg 22.0186209085317,19.8692515543133 --qseq -p 3 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s --- Summary --- 687s Read 1 reference strings 687s Checked 15 alignments, 0 edits 687s --------------- 687s PASSED 687s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 687s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 687s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 687s 48 reads; of these: 687s 48 (100.00%) were unpaired; of these: 687s 33 (68.75%) aligned 0 times 687s 12 (25.00%) aligned exactly 1 time 687s 3 (6.25%) aligned >1 times 687s 31.25% overall alignment rate 687s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 687s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 687s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 687s Flattened IUPAC characters 687s Mutating sequence Sim.pm.1 687s Introducing 23 SNPs, 3/3 ref/read gaps, and 1 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutating sequence Sim.pm.2 687s Introducing 3 SNPs, 6/0 ref/read gaps, and 1 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutated reference genome to subject genome 687s SNPs introduced: 26 687s Reference gaps introduced: 9 687s Read gaps introduced: 3 687s Rearrangements introduced: 2 687s Created read sampler 687s Sampling 132 reads 687s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 687s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 687s parsing sequence Sim.pm.1... 687s parsing sequence Sim.pm.2... 687s Parsed 234 reference bases 687s *** Run 13 of 100 687s /usr/bin/bowtie2 --rfg 29.9661051631528,11.2561374626922 -R 1 --score-min L,9.95024518006055,5.23539337935319 --cp-ival 2 --local --trim5 4 --large-index -M 2 --cp-min 7 -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw 687s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 687s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '2' because it was < 2 characters long 687s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '11' because it was < 2 characters long 687s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '12' because it was < 2 characters long 687s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '20' because it was < 2 characters long 687s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '21' because it was < 2 characters long 687s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '54' because it was < 2 characters long 687s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '55' because it was < 2 characters long 687s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '58' because it was < 2 characters long 687s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '59' because it was < 2 characters long 687s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '66' because it was < 2 characters long 687s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '69' because it was < 2 characters long 687s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '80' because it was < 2 characters long 687s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '89' because it was < 2 characters long 687s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '98' because it was < 2 characters long 687s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '99' because it was < 2 characters long 687s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '103' because it was < 2 characters long 687s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '105' because it was < 2 characters long 687s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '113' because it was < 2 characters long 687s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '118' because it was < 2 characters long 687s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '122' because it was < 2 characters long 687s Warning: skipping read '123' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '123' because it was < 2 characters long 687s Warning: skipping read '130' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '130' because it was < 2 characters long 687s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '131' because it was < 2 characters long 687s 132 reads; of these: 687s 132 (100.00%) were unpaired; of these: 687s 132 (100.00%) aligned 0 times 687s 0 (0.00%) aligned exactly 1 time 687s 0 (0.00%) aligned >1 times 687s 0.00% overall alignment rate 687s Read 50 alignments... 687s Read 100 alignments... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s --- Summary --- 687s Read 1 reference strings 687s Checked 0 alignments, 0 edits 687s --------------- 687s PASSED 687s ALSO checking that bowtie2 and bowtie2-align match up 687s /usr/bin/bowtie2 --rfg 29.9661051631528,11.2561374626922 -R 1 --score-min L,9.95024518006055,5.23539337935319 --cp-ival 2 --local --trim5 4 --large-index -M 2 --cp-min 7 -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 687s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 687s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '2' because it was < 2 characters long 687s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '11' because it was < 2 characters long 687s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '12' because it was < 2 characters long 687s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '20' because it was < 2 characters long 687s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '21' because it was < 2 characters long 687s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '54' because it was < 2 characters long 687s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '55' because it was < 2 characters long 687s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '58' because it was < 2 characters long 687s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '59' because it was < 2 characters long 687s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '66' because it was < 2 characters long 687s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '69' because it was < 2 characters long 687s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '80' because it was < 2 characters long 687s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '89' because it was < 2 characters long 687s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '98' because it was < 2 characters long 687s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '99' because it was < 2 characters long 687s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '103' because it was < 2 characters long 687s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '105' because it was < 2 characters long 687s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '113' because it was < 2 characters long 687s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '118' because it was < 2 characters long 687s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '122' because it was < 2 characters long 687s Warning: skipping read '123' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '123' because it was < 2 characters long 687s Warning: skipping read '130' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '130' because it was < 2 characters long 687s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '131' because it was < 2 characters long 687s 132 reads; of these: 687s 132 (100.00%) were unpaired; of these: 687s 132 (100.00%) aligned 0 times 687s 0 (0.00%) aligned exactly 1 time 687s 0 (0.00%) aligned >1 times 687s 0.00% overall alignment rate 687s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 687s Flattened IUPAC characters 687s Mutating sequence Sim.pm.1 687s Introducing 14 SNPs, 2/1 ref/read gaps, and 0 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutating sequence Sim.pm.2 687s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutated reference genome to subject genome 687s SNPs introduced: 17 687s Reference gaps introduced: 2 687s Read gaps introduced: 1 687s Rearrangements introduced: 1 687s Created read sampler 687s Sampling 94 reads 687s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 687s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 687s parsing sequence Sim.pm.1... 687s parsing sequence Sim.pm.2... 687s Parsed 234 reference bases 687s *** Run 14 of 100 687s /usr/bin/bowtie2 --score-min L,6.05353864633981,8.93278446713774 -D 7 -k 9 --large-index --cp-min 8 --trim3 6 --mp 7.63570442145452,5.49835369147363 --rfg 13.1389790744582,18.5048423520809 --n-ceil 0.929584161152436,0.749144923955816 --trim5 9 --local --cp-ival 1 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 687s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '1' because it was < 2 characters long 687s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '6' because it was < 2 characters long 687s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '9' because it was < 2 characters long 687s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '11' because it was < 2 characters long 687s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '17' because it was < 2 characters long 687s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '18' because it was < 2 characters long 687s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '20' because it was < 2 characters long 687s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '21' because it was < 2 characters long 687s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '25' because it was < 2 characters long 687s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '26' because it was < 2 characters long 687s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '27' because it was < 2 characters long 687s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '29' because it was < 2 characters long 687s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '30' because it was < 2 characters long 687s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '35' because it was < 2 characters long 687s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '36' because it was < 2 characters long 687s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '38' because it was < 2 characters long 687s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '40' because it was < 2 characters long 687s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '41' because it was < 2 characters long 687s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 687s Warning: skipping read '42' because it was < 2 characters long 687s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '43' because it was < 2 characters long 687s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '47' because it was < 2 characters long 687s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '48' because it was < 2 characters long 687s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '49' because it was < 2 characters long 687s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '51' because it was < 2 characters long 687s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '52' because it was < 2 characters long 687s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '57' because it was < 2 characters long 687s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '61' because it was < 2 characters long 687s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '63' because it was < 2 characters long 687s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '64' because it was < 2 characters long 687s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '68' because it was < 2 characters long 687s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '78' because it was < 2 characters long 687s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '84' because it was < 2 characters long 687s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '86' because it was < 2 characters long 687s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '89' because it was < 2 characters long 687s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '91' because it was < 2 characters long 687s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 687s Warning: skipping read '94' because it was < 2 characters long 687s 94 reads; of these: 687s 94 (100.00%) were unpaired; of these: 687s 94 (100.00%) aligned 0 times 687s 0 (0.00%) aligned exactly 1 time 687s 0 (0.00%) aligned >1 times 687s 0.00% overall alignment rate 687s Read 50 alignments... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s --- Summary --- 687s Read 1 reference strings 687s Checked 0 alignments, 0 edits 687s --------------- 687s PASSED 687s Flattened IUPAC characters 687s Mutating sequence Sim.pm.2 687s Introducing 12 SNPs, 1/1 ref/read gaps, and 2 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutating sequence Sim.pm.1 687s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutated reference genome to subject genome 687s SNPs introduced: 15 687s Reference gaps introduced: 1 687s Read gaps introduced: 1 687s Rearrangements introduced: 3 687s Created read sampler 687s Sampling 155 reads 687s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 687s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 687s parsing sequence Sim.pm.1... 687s parsing sequence Sim.pm.2... 687s Parsed 234 reference bases 687s *** Run 15 of 100 687s /usr/bin/bowtie2 --rdg 48.1157438218772,9.72206394252155 --ma 7.74976410145403 --score-min L,3.48362954757573,2.79533180529401 -R 1 --cp-min 7 --large-index --nofw -i C,3.17367969768251,4.17526739505014 --cp-ival 1 -a --trim5 3 --norc --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq 687s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (1) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 687s Warning: skipping read 'R_1_1_1_126_126_1/1' because length (1) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_148_148_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_151_151_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_153_153_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_154_154_1/1; setting to 0 instead 687s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_155_155_1/1; setting to 0 instead 687s Read 50 alignments... 687s 155 reads; of these: 687s 155 (100.00%) were unpaired; of these: 687s 155 (100.00%) aligned 0 times 687s 0 (0.00%) aligned exactly 1 time 687s 0 (0.00%) aligned >1 times 687s 0.00% overall alignment rate 687s Read 100 alignments... 687s Read 150 alignments... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s --- Summary --- 687s Read 1 reference strings 687s Checked 0 alignments, 0 edits 687s --------------- 687s PASSED 687s Flattened IUPAC characters 687s Mutating sequence Sim.pm.2 687s Introducing 6 SNPs, 0/2 ref/read gaps, and 3 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutating sequence Sim.pm.1 687s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutated reference genome to subject genome 687s SNPs introduced: 12 687s Reference gaps introduced: 0 687s Read gaps introduced: 2 687s Rearrangements introduced: 3 687s Created read sampler 687s Sampling 34 reads 687s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 687s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 687s parsing sequence Sim.pm.1... 687s parsing sequence Sim.pm.2... 687s *** Run 16 of 100 687s /usr/bin/bowtie2 --large-index --np 2 --cp-min 5 --mm --score-min L,5.63988558966214,9.29310249114116 -D 42 --local --cp-ival 1 -a --trim5 4 --rfg 9.1278937099832 --trim3 0 --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq 687s Parsed 234 reference bases 687s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 687s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 687s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 687s 34 reads; of these: 687s 34 (100.00%) were unpaired; of these: 687s 34 (100.00%) aligned 0 times 687s 0 (0.00%) aligned exactly 1 time 687s 0 (0.00%) aligned >1 times 687s 0.00% overall alignment rate 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s Processing line... 687s --- Summary --- 687s Read 1 reference strings 687s Checked 0 alignments, 0 edits 687s --------------- 687s PASSED 687s Flattened IUPAC characters 687s Mutating sequence Sim.pm.2 687s Introducing 1 SNPs, 1/1 ref/read gaps, and 2 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutating sequence Sim.pm.1 687s Introducing 10 SNPs, 1/0 ref/read gaps, and 0 rearrangements 687s Finished SNPs 687s Finished ref gaps 687s Finished read gaps 687s Mutated reference genome to subject genome 687s SNPs introduced: 11 687s Reference gaps introduced: 2 687s Read gaps introduced: 1 687s Rearrangements introduced: 2 687s Created read sampler 687s Sampling 102 reads 687s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 687s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 687s parsing sequence Sim.pm.1... 687s parsing sequence Sim.pm.2... 687s Parsed 234 reference bases 687s *** Run 17 of 100 687s /usr/bin/bowtie2 --trim3 0 --nofw --rfg 6.84263404674078,11.2835490056787 -a --cp-ival 2 --gbar 3 --ma 6.70992548453792 --score-min L,6.67390166003334,8.41327817837179 --rdg 39.1357928465784,5.88691453700314 --cp-min 3 --np 3 --large-index --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq 688s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 688s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 688s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 688s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 688s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 688s Read 50 alignments... 688s Read 100 alignments... 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 688s Warning: skipping mate #2 of read 'R_1_1_1_85_85_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #2 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 688s Read 150 alignments... 688s 102 reads; of these: 688s 102 (100.00%) were paired; of these: 688s 101 (99.02%) aligned concordantly 0 times 688s 0 (0.00%) aligned concordantly exactly 1 time 688s 1 (0.98%) aligned concordantly >1 times 688s ---- 688s 101 pairs aligned concordantly 0 times; of these: 688s 1 (0.99%) aligned discordantly 1 time 688s ---- 688s 100 pairs aligned 0 times concordantly or discordantly; of these: 688s 200 mates make up the pairs; of these: 688s 181 (90.50%) aligned 0 times 688s 14 (7.00%) aligned exactly 1 time 688s 5 (2.50%) aligned >1 times 688s 11.27% overall alignment rate 688s Read 200 alignments... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s GGTCTCAGGTTGGAGTCCCGCGGCCCGTT 688s GGTCTCAGGTTGGAGTCCCGCGGCCCGTT 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s AACG 688s AACG 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s AGGCCGTTGGGGTTCG 688s AGGCCGTTGGGGTTCG 688s Processing line... 688s Processing line... 688s CGA 688s CGA 688s Processing line... 688s Processing line... 688s CGGTTGGTTTATGTCATC 688s CGGTTGGTTTATGTCATC 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s GTAGGCCGTTGGGGTT 688s GTAGGCCGTTGGGGTT 688s Processing line... 688s GTAGGCCGTTGGGGTT 688s GTAGGCCGTTGGGGTT 688s Processing line... 688s Processing line... 688s GGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCG 688s GGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCG 688s Processing line... 688s Processing line... 688s GGCGTGGGTGCGGCGGGGCCAGTTC 688s GGCGTGGGTGCGGCGGGGCCAGTTC 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s GGCCAGTTCGATTCGG 688s GGCCAGTTCGATTCGG 688s Processing line... 688s Processing line... 688s GTTTG 688s GTTTG 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s GTC 688s GTC 688s Processing line... 688s GCC 688s GCC 688s Processing line... 688s GTC 688s GTC 688s Processing line... 688s GCC 688s GCC 688s Processing line... 688s GTC 688s GTC 688s Processing line... 688s GCC 688s GCC 688s Processing line... 688s GTC 688s GTC 688s Processing line... 688s GCC 688s GCC 688s Processing line... 688s GTC 688s GTC 688s Processing line... 688s GCC 688s GCC 688s Processing line... 688s GTC 688s GTC 688s Processing line... 688s GCC 688s GCC 688s Processing line... 688s GTC 688s GTC 688s Processing line... 688s GCC 688s GCC 688s Processing line... 688s Processing line... 688s Processing line... 688s CCC 688s CCC 688s Processing line... 688s CCC 688s CCC 688s Processing line... 688s CCC 688s CCC 688s Processing line... 688s CCC 688s CCC 688s Processing line... 688s CCC 688s CCC 688s Processing line... 688s Processing line... 688s CCGTTCCCGGTGTGTCGTTGTAGGCCGTTG 688s CCGTTCCCGGTGTGTCGTTGTAGGCCGTTG 688s Processing line... 688s CCGTTCCCGGTGTGTCGTTGTAGGCCGTTG 688s CCGTTCCCGGTGTGTCGTTGTAGGCCGTTG 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s TCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTT 688s TCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTT 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s GGGCGTGGGTGCGGCGGGGCCAGTTCGAT 688s GGGCGTGGGTGCGGCGGGGCCAGTTCGAT 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s GTTGGTTTATGTCATCGCGCG 688s GTTGGTTTATGTCATCGCGCG 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s CGCGCGGTT 688s CGCGCGGTT 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s CGCCGTTCCCGG 688s CGCCGTTCCCGG 688s Processing line... 688s CGCCGTTCCCGG 688s CGCCGTTCCCGG 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s TGAC 688s TGAC 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s TATGTCAT 688s TATGTCAT 688s Processing line... 688s CGCGGTTGTTTGGTGTG 688s CGCGGTTGTTTGGTGTG 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s GGC 688s GGC 688s Processing line... 688s GGC 688s GGC 688s Processing line... 688s GGC 688s GGC 688s Processing line... 688s GGC 688s GGC 688s Processing line... 688s GGC 688s GGC 688s Processing line... 688s GGC 688s GGC 688s Processing line... 688s GGC 688s GGC 688s /usr/bin/bowtie2 --trim3 0 --nofw --rfg 6.84263404674078,11.2835490056787 -a --cp-ival 2 --gbar 3 --ma 6.70992548453792 --score-min L,6.67390166003334,8.41327817837179 --rdg 39.1357928465784,5.88691453700314 --cp-min 3 --np 3 --large-index --qseq -p 2 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 688s Processing line... 688s GGC 688s GGC 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s --- Summary --- 688s Read 1 reference strings 688s Checked 49 alignments, 0 edits 688s --------------- 688s PASSED 688s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 688s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 688s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 688s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 688s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 688s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 688s Warning: skipping mate #2 of read 'R_1_1_1_85_85_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #2 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 688s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 688s 102 reads; of these: 688s 102 (100.00%) were paired; of these: 688s 101 (99.02%) aligned concordantly 0 times 688s 0 (0.00%) aligned concordantly exactly 1 time 688s 1 (0.98%) aligned concordantly >1 times 688s ---- 688s 101 pairs aligned concordantly 0 times; of these: 688s 1 (0.99%) aligned discordantly 1 time 688s ---- 688s 100 pairs aligned 0 times concordantly or discordantly; of these: 688s 200 mates make up the pairs; of these: 688s 181 (90.50%) aligned 0 times 688s 14 (7.00%) aligned exactly 1 time 688s 5 (2.50%) aligned >1 times 688s 11.27% overall alignment rate 688s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 688s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 688s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 688s Flattened IUPAC characters 688s Mutating sequence Sim.pm.2 688s Introducing 20 SNPs, 0/0 ref/read gaps, and 1 rearrangements 688s Finished SNPs 688s Finished ref gaps 688s Finished read gaps 688s Mutating sequence Sim.pm.1 688s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 688s Finished SNPs 688s Finished ref gaps 688s Finished read gaps 688s Mutated reference genome to subject genome 688s SNPs introduced: 23 688s Reference gaps introduced: 0 688s Read gaps introduced: 0 688s Rearrangements introduced: 1 688s Created read sampler 688s Sampling 46 reads 688s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 688s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 688s parsing sequence Sim.pm.1... 688s parsing sequence Sim.pm.2... 688s Parsed 234 reference bases 688s *** Run 18 of 100 688s /usr/bin/bowtie2 -a --n-ceil 1.04428866168695,1.33090999705128 --local --cp-ival 1 --trim3 2 --nofw --large-index --cp-min 2 --np 1 --score-min L,3.98424550269771,9.26620119932439 -D 10 --rdg 17.9879191480452 --mm -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 688s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #2 of read '6' because it was < 2 characters long 688s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '30' because it was < 2 characters long 688s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #2 of read '32' because it was < 2 characters long 688s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '38' because it was < 2 characters long 688s 46 reads; of these: 688s 43 (93.48%) were paired; of these: 688s 43 (100.00%) aligned concordantly 0 times 688s 0 (0.00%) aligned concordantly exactly 1 time 688s 0 (0.00%) aligned concordantly >1 times 688s ---- 688s 43 pairs aligned concordantly 0 times; of these: 688s 0 (0.00%) aligned discordantly 1 time 688s ---- 688s 43 pairs aligned 0 times concordantly or discordantly; of these: 688s 86 mates make up the pairs; of these: 688s 86 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 3 (6.52%) were unpaired; of these: 688s 3 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 0.00% overall alignment rate 688s Read 50 alignments... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s --- Summary --- 688s Read 1 reference strings 688s Checked 0 alignments, 0 edits 688s --------------- 688s PASSED 688s ALSO checking that bowtie2 and bowtie2-align match up 688s /usr/bin/bowtie2 -a --n-ceil 1.04428866168695,1.33090999705128 --local --cp-ival 1 --trim3 2 --nofw --large-index --cp-min 2 --np 1 --score-min L,3.98424550269771,9.26620119932439 -D 10 --rdg 17.9879191480452 --mm -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 688s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #2 of read '6' because it was < 2 characters long 688s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '30' because it was < 2 characters long 688s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #2 of read '32' because it was < 2 characters long 688s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '38' because it was < 2 characters long 688s 46 reads; of these: 688s 43 (93.48%) were paired; of these: 688s 43 (100.00%) aligned concordantly 0 times 688s 0 (0.00%) aligned concordantly exactly 1 time 688s 0 (0.00%) aligned concordantly >1 times 688s ---- 688s 43 pairs aligned concordantly 0 times; of these: 688s 0 (0.00%) aligned discordantly 1 time 688s ---- 688s 43 pairs aligned 0 times concordantly or discordantly; of these: 688s 86 mates make up the pairs; of these: 688s 86 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 3 (6.52%) were unpaired; of these: 688s 3 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 0.00% overall alignment rate 688s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 688s *** Run 19 of 100 688s /usr/bin/bowtie2 --gbar 1 --score-min L,6.45446522004416,5.97475667430755 --np 8 --cp-min 4 --large-index -i S,0.0321769512887303 --cp-ival 1 --local --trim5 4 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq 688s Flattened IUPAC characters 688s Mutating sequence Sim.pm.2 688s Introducing 25 SNPs, 2/1 ref/read gaps, and 2 rearrangements 688s Finished SNPs 688s Finished ref gaps 688s Finished read gaps 688s Mutating sequence Sim.pm.1 688s Introducing 7 SNPs, 2/0 ref/read gaps, and 1 rearrangements 688s Finished SNPs 688s Finished ref gaps 688s Finished read gaps 688s Mutated reference genome to subject genome 688s SNPs introduced: 32 688s Reference gaps introduced: 4 688s Read gaps introduced: 1 688s Rearrangements introduced: 3 688s Created read sampler 688s Sampling 42 reads 688s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 688s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 688s parsing sequence Sim.pm.1... 688s parsing sequence Sim.pm.2... 688s Parsed 234 reference bases 688s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 688s 42 reads; of these: 688s 38 (90.48%) were paired; of these: 688s 38 (100.00%) aligned concordantly 0 times 688s 0 (0.00%) aligned concordantly exactly 1 time 688s 0 (0.00%) aligned concordantly >1 times 688s ---- 688s 38 pairs aligned concordantly 0 times; of these: 688s 0 (0.00%) aligned discordantly 1 time 688s ---- 688s 38 pairs aligned 0 times concordantly or discordantly; of these: 688s 76 mates make up the pairs; of these: 688s 76 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 4 (9.52%) were unpaired; of these: 688s 4 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 0.00% overall alignment rate 688s Read 50 alignments... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s --- Summary --- 688s Read 1 reference strings 688s Checked 0 alignments, 0 edits 688s --------------- 688s PASSED 688s ALSO checking that bowtie2 and bowtie2-align match up 688s /usr/bin/bowtie2 --gbar 1 --score-min L,6.45446522004416,5.97475667430755 --np 8 --cp-min 4 --large-index -i S,0.0321769512887303 --cp-ival 1 --local --trim5 4 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 688s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 688s 42 reads; of these: 688s 38 (90.48%) were paired; of these: 688s 38 (100.00%) aligned concordantly 0 times 688s 0 (0.00%) aligned concordantly exactly 1 time 688s 0 (0.00%) aligned concordantly >1 times 688s ---- 688s 38 pairs aligned concordantly 0 times; of these: 688s 0 (0.00%) aligned discordantly 1 time 688s ---- 688s 38 pairs aligned 0 times concordantly or discordantly; of these: 688s 76 mates make up the pairs; of these: 688s 76 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 4 (9.52%) were unpaired; of these: 688s 4 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 0.00% overall alignment rate 688s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 688s Flattened IUPAC characters 688s Mutating sequence Sim.pm.2 688s Introducing 9 SNPs, 0/0 ref/read gaps, and 1 rearrangements 688s Finished SNPs 688s Finished ref gaps 688s Finished read gaps 688s Mutating sequence Sim.pm.1 688s Introducing 4 SNPs, 0/2 ref/read gaps, and 0 rearrangements 688s Finished SNPs 688s Finished ref gaps 688s Finished read gaps 688s Mutated reference genome to subject genome 688s SNPs introduced: 13 688s Reference gaps introduced: 0 688s *** Run 20 of 100 688s /usr/bin/bowtie2 --gbar 2 --score-min L,6.09937045045499,3.67808129342129 --mm --cp-min 3 --large-index --mp 9.92159848256776,3.5848701259652 --trim3 8 --rfg 37.482244307171 --norc --trim5 3 --cp-ival 1 --local -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta 688s Read gaps introduced: 2 688s Rearrangements introduced: 1 688s Created read sampler 688s Sampling 48 reads 688s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 688s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 688s parsing sequence Sim.pm.1... 688s parsing sequence Sim.pm.2... 688s Parsed 234 reference bases 688s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '7' because it was < 2 characters long 688s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '13' because it was < 2 characters long 688s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '18' because it was < 2 characters long 688s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '19' because it was < 2 characters long 688s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '23' because it was < 2 characters long 688s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '31' because it was < 2 characters long 688s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '33' because it was < 2 characters long 688s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 688s Warning: skipping read '34' because it was < 2 characters long 688s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '35' because it was < 2 characters long 688s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '36' because it was < 2 characters long 688s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 688s Warning: skipping read '38' because it was < 2 characters long 688s /usr/bin/bowtie2 --gbar 2 --score-min L,6.09937045045499,3.67808129342129 --mm --cp-min 3 --large-index --mp 9.92159848256776,3.5848701259652 --trim3 8 --rfg 37.482244307171 --norc --trim5 3 --cp-ival 1 --local -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 688s 48 reads; of these: 688s 40 (83.33%) were paired; of these: 688s 40 (100.00%) aligned concordantly 0 times 688s 0 (0.00%) aligned concordantly exactly 1 time 688s 0 (0.00%) aligned concordantly >1 times 688s ---- 688s 40 pairs aligned concordantly 0 times; of these: 688s 0 (0.00%) aligned discordantly 1 time 688s ---- 688s 40 pairs aligned 0 times concordantly or discordantly; of these: 688s 80 mates make up the pairs; of these: 688s 80 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 8 (16.67%) were unpaired; of these: 688s 8 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 0.00% overall alignment rate 688s Read 50 alignments... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s --- Summary --- 688s Read 1 reference strings 688s Checked 0 alignments, 0 edits 688s --------------- 688s PASSED 688s ALSO checking that bowtie2 and bowtie2-align match up 688s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '7' because it was < 2 characters long 688s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '13' because it was < 2 characters long 688s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '18' because it was < 2 characters long 688s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '19' because it was < 2 characters long 688s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '23' because it was < 2 characters long 688s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '31' because it was < 2 characters long 688s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '33' because it was < 2 characters long 688s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 688s Warning: skipping read '34' because it was < 2 characters long 688s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '35' because it was < 2 characters long 688s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '36' because it was < 2 characters long 688s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 688s Warning: skipping read '38' because it was < 2 characters long 688s 48 reads; of these: 688s 40 (83.33%) were paired; of these: 688s 40 (100.00%) aligned concordantly 0 times 688s 0 (0.00%) aligned concordantly exactly 1 time 688s 0 (0.00%) aligned concordantly >1 times 688s ---- 688s 40 pairs aligned concordantly 0 times; of these: 688s 0 (0.00%) aligned discordantly 1 time 688s ---- 688s 40 pairs aligned 0 times concordantly or discordantly; of these: 688s 80 mates make up the pairs; of these: 688s 80 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 8 (16.67%) were unpaired; of these: 688s 8 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 0.00% overall alignment rate 688s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 688s /usr/bin/bowtie2 --gbar 2 --score-min L,6.09937045045499,3.67808129342129 --mm --cp-min 3 --large-index --mp 9.92159848256776,3.5848701259652 --trim3 8 --rfg 37.482244307171 --norc --trim5 3 --cp-ival 1 --local -f -p 4 -x /tmp/Sim.pm.RKKEKvBt --reorder -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 688s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 688s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '7' because it was < 2 characters long 688s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '13' because it was < 2 characters long 688s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '18' because it was < 2 characters long 688s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '19' because it was < 2 characters long 688s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '23' because it was < 2 characters long 688s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '31' because it was < 2 characters long 688s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '33' because it was < 2 characters long 688s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 688s Warning: skipping read '34' because it was < 2 characters long 688s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '35' because it was < 2 characters long 688s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read '36' because it was < 2 characters long 688s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 688s Warning: skipping read '38' because it was < 2 characters long 688s 48 reads; of these: 688s 40 (83.33%) were paired; of these: 688s 40 (100.00%) aligned concordantly 0 times 688s 0 (0.00%) aligned concordantly exactly 1 time 688s 0 (0.00%) aligned concordantly >1 times 688s ---- 688s 40 pairs aligned concordantly 0 times; of these: 688s 0 (0.00%) aligned discordantly 1 time 688s ---- 688s 40 pairs aligned 0 times concordantly or discordantly; of these: 688s 80 mates make up the pairs; of these: 688s 80 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 8 (16.67%) were unpaired; of these: 688s 8 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 0.00% overall alignment rate 688s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 688s Flattened IUPAC characters 688s Mutating sequence Sim.pm.2 688s Introducing 10 SNPs, 2/1 ref/read gaps, and 0 rearrangements 688s Finished SNPs 688s Finished ref gaps 688s Finished read gaps 688s Mutating sequence Sim.pm.1 688s Introducing 10 SNPs, 0/1 ref/read gaps, and 0 rearrangements 688s Finished SNPs 688s Finished ref gaps 688s Finished read gaps 688s Mutated reference genome to subject genome 688s SNPs introduced: 20 688s Reference gaps introduced: 2 688s Read gaps introduced: 2 688s Rearrangements introduced: 0 688s Created read sampler 688s Sampling 120 reads 688s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 688s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 688s parsing sequence Sim.pm.1... 688s *** Run 21 of 100 688s /usr/bin/bowtie2 --n-ceil 0.646206739092047,0.0100832329397438 --trim5 0 --norc --cp-ival 1 --local --nofw --trim3 8 --np 4 --cp-min 4 --large-index --score-min L,6.30309201579673,7.0569549183553 --rdg 14.2281733296787,6.12797987082894 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq 688s parsing sequence Sim.pm.2... 688s Parsed 234 reference bases 688s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 688s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 688s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #2 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 688s Warning: skipping mate #2 of read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #2 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 688s Read 50 alignments... 688s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 688s Warning: skipping read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 688s Warning: skipping mate #2 of read 'R_1_1_1_109_109_1/1' because length (1) <= # seed mismatches (0) 688s Warning: skipping mate #2 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 688s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 688s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 688s Read 100 alignments... 688s 120 reads; of these: 688s 102 (85.00%) were paired; of these: 688s 102 (100.00%) aligned concordantly 0 times 688s 0 (0.00%) aligned concordantly exactly 1 time 688s 0 (0.00%) aligned concordantly >1 times 688s ---- 688s 102 pairs aligned concordantly 0 times; of these: 688s 0 (0.00%) aligned discordantly 1 time 688s ---- 688s 102 pairs aligned 0 times concordantly or discordantly; of these: 688s 204 mates make up the pairs; of these: 688s 204 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 18 (15.00%) were unpaired; of these: 688s 18 (100.00%) aligned 0 times 688s 0 (0.00%) aligned exactly 1 time 688s 0 (0.00%) aligned >1 times 688s 0.00% overall alignment rate 688s Read 150 alignments... 688s Read 200 alignments... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s Processing line... 688s --- Summary --- 688s Read 1 reference strings 688s Checked 0 alignments, 0 edits 688s --------------- 688s PASSED 688s Flattened IUPAC characters 688s Mutating sequence Sim.pm.2 688s Introducing 10 SNPs, 1/0 ref/read gaps, and 0 rearrangements 688s Finished SNPs 688s Finished ref gaps 688s Finished read gaps 688s Mutating sequence Sim.pm.1 688s Introducing 7 SNPs, 2/0 ref/read gaps, and 2 rearrangements 688s Finished SNPs 688s Finished ref gaps 688s Finished read gaps 688s Mutated reference genome to subject genome 688s SNPs introduced: 17 688s Reference gaps introduced: 3 688s Read gaps introduced: 0 688s Rearrangements introduced: 2 688s Created read sampler 688s Sampling 78 reads 688s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 688s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 688s parsing sequence Sim.pm.1... 688s parsing sequence Sim.pm.2... 688s Parsed 234 reference bases 688s *** Run 22 of 100 688s /usr/bin/bowtie2 --score-min L,4.26074803302231,7.71182112000175 --rdg 30.7762298127541,12.3487313364829 --large-index --cp-min 5 --np 2 --trim3 5 --mp 7.88530883670377,4.9125117527151 -M 3 --trim5 3 --n-ceil 0.963364262546395,1.47968008032665 --local --cp-ival 2 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 689s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 689s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '1' because it was < 2 characters long 689s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 689s Warning: skipping read '11' because it was < 2 characters long 689s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '25' because it was < 2 characters long 689s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '27' because it was < 2 characters long 689s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '30' because it was < 2 characters long 689s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '36' because it was < 2 characters long 689s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '37' because it was < 2 characters long 689s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '44' because it was < 2 characters long 689s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '52' because it was < 2 characters long 689s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '61' because it was < 2 characters long 689s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '63' because it was < 2 characters long 689s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '67' because it was < 2 characters long 689s 78 reads; of these: 689s 78 (100.00%) were unpaired; of these: 689s 78 (100.00%) aligned 0 times 689s 0 (0.00%) aligned exactly 1 time 689s 0 (0.00%) aligned >1 times 689s 0.00% overall alignment rate 689s Read 50 alignments... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s /usr/bin/bowtie2 --score-min L,4.26074803302231,7.71182112000175 --rdg 30.7762298127541,12.3487313364829 --large-index --cp-min 5 --np 2 --trim3 5 --mp 7.88530883670377,4.9125117527151 -M 3 --trim5 3 --n-ceil 0.963364262546395,1.47968008032665 --local --cp-ival 2 -q -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s --- Summary --- 689s Read 1 reference strings 689s Checked 0 alignments, 0 edits 689s --------------- 689s PASSED 689s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 689s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 689s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '1' because it was < 2 characters long 689s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 689s Warning: skipping read '11' because it was < 2 characters long 689s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '25' because it was < 2 characters long 689s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '27' because it was < 2 characters long 689s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '30' because it was < 2 characters long 689s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '36' because it was < 2 characters long 689s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '37' because it was < 2 characters long 689s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '44' because it was < 2 characters long 689s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '52' because it was < 2 characters long 689s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '61' because it was < 2 characters long 689s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '63' because it was < 2 characters long 689s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '67' because it was < 2 characters long 689s 78 reads; of these: 689s 78 (100.00%) were unpaired; of these: 689s 78 (100.00%) aligned 0 times 689s 0 (0.00%) aligned exactly 1 time 689s 0 (0.00%) aligned >1 times 689s 0.00% overall alignment rate 689s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 689s Flattened IUPAC characters 689s Mutating sequence Sim.pm.2 689s Introducing 16 SNPs, 1/0 ref/read gaps, and 1 rearrangements 689s Finished SNPs 689s Finished ref gaps 689s Finished read gaps 689s Mutating sequence Sim.pm.1 689s Introducing 12 SNPs, 1/4 ref/read gaps, and 0 rearrangements 689s Finished SNPs 689s Finished ref gaps 689s Finished read gaps 689s Mutated reference genome to subject genome 689s SNPs introduced: 28 689s Reference gaps introduced: 2 689s Read gaps introduced: 4 689s Rearrangements introduced: 1 689s Created read sampler 689s Sampling 123 reads 689s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 689s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 689s parsing sequence Sim.pm.1... 689s *** Run 23 of 100 689s /usr/bin/bowtie2 --local --cp-ival 1 --np 2 --cp-min 6 --large-index --trim3 2 --score-min L,2.53810028533383,4.28046975510192 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 689s parsing sequence Sim.pm.2... 689s Parsed 234 reference bases 689s Warning: skipping mate #1 of read '34' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #1 of read '34' because it was < 2 characters long 689s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 689s Warning: skipping mate #1 of read '41' because it was < 2 characters long 689s Read 50 alignments... 689s Read 100 alignments... 689s Warning: skipping mate #2 of read '68' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #2 of read '68' because it was < 2 characters long 689s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #1 of read '70' because it was < 2 characters long 689s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #2 of read '71' because it was < 2 characters long 689s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #2 of read '89' because it was < 2 characters long 689s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 689s Warning: skipping mate #1 of read '118' because it was < 2 characters long 689s 123 reads; of these: 689s 119 (96.75%) were paired; of these: 689s 119 (100.00%) aligned concordantly 0 times 689s 0 (0.00%) aligned concordantly exactly 1 time 689s 0 (0.00%) aligned concordantly >1 times 689s ---- 689s 119 pairs aligned concordantly 0 times; of these: 689s 0 (0.00%) aligned discordantly 1 time 689s ---- 689s 119 pairs aligned 0 times concordantly or discordantly; of these: 689s 238 mates make up the pairs; of these: 689s 238 (100.00%) aligned 0 times 689s 0 (0.00%) aligned exactly 1 time 689s 0 (0.00%) aligned >1 times 689s 4 (3.25%) were unpaired; of these: 689s 4 (100.00%) aligned 0 times 689s 0 (0.00%) aligned exactly 1 time 689s 0 (0.00%) aligned >1 times 689s 0.00% overall alignment rate 689s Read 150 alignments... 689s Read 200 alignments... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 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Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s /usr/bin/bowtie2 --local --cp-ival 1 --np 2 --cp-min 6 --large-index --trim3 2 --score-min L,2.53810028533383,4.28046975510192 -q -p 3 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 689s --- Summary --- 689s Read 1 reference strings 689s Checked 0 alignments, 0 edits 689s --------------- 689s PASSED 689s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 689s Warning: skipping mate #1 of read '34' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #1 of read '34' because it was < 2 characters long 689s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 689s Warning: skipping mate #1 of read '41' because it was < 2 characters long 689s Warning: skipping mate #2 of read '68' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #2 of read '68' because it was < 2 characters long 689s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #1 of read '70' because it was < 2 characters long 689s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #2 of read '71' because it was < 2 characters long 689s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #2 of read '89' because it was < 2 characters long 689s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 689s Warning: skipping mate #1 of read '118' because it was < 2 characters long 689s 123 reads; of these: 689s 119 (96.75%) were paired; of these: 689s 119 (100.00%) aligned concordantly 0 times 689s 0 (0.00%) aligned concordantly exactly 1 time 689s 0 (0.00%) aligned concordantly >1 times 689s ---- 689s 119 pairs aligned concordantly 0 times; of these: 689s 0 (0.00%) aligned discordantly 1 time 689s ---- 689s 119 pairs aligned 0 times concordantly or discordantly; of these: 689s 238 mates make up the pairs; of these: 689s 238 (100.00%) aligned 0 times 689s 0 (0.00%) aligned exactly 1 time 689s 0 (0.00%) aligned >1 times 689s 4 (3.25%) were unpaired; of these: 689s 4 (100.00%) aligned 0 times 689s 0 (0.00%) aligned exactly 1 time 689s 0 (0.00%) aligned >1 times 689s 0.00% overall alignment rate 689s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 689s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 689s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 689s Flattened IUPAC characters 689s Mutating sequence Sim.pm.2 689s Introducing 16 SNPs, 3/1 ref/read gaps, and 1 rearrangements 689s Finished SNPs 689s Finished ref gaps 689s Finished read gaps 689s Mutating sequence Sim.pm.1 689s Introducing 11 SNPs, 0/2 ref/read gaps, and 3 rearrangements 689s Finished SNPs 689s Finished ref gaps 689s Finished read gaps 689s Mutated reference genome to subject genome 689s SNPs introduced: 27 689s Reference gaps introduced: 3 689s *** Run 24 of 100 689s /usr/bin/bowtie2 --cp-min 5 --large-index --cp-ival 2 --local --mp 8.23022594701928,7.28389115032309 --gbar 1 --score-min L,8.07461839790576,4.45669908347513 --rfg 2.64059455154954 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq 689s Read gaps introduced: 3 689s Rearrangements introduced: 4 689s Created read sampler 689s Sampling 48 reads 689s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 689s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 689s parsing sequence Sim.pm.1... 689s parsing sequence Sim.pm.2... 689s Parsed 234 reference bases 689s Warning: skipping mate #2 of read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #2 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 689s 48 reads; of these: 689s 48 (100.00%) were paired; of these: 689s 48 (100.00%) aligned concordantly 0 times 689s 0 (0.00%) aligned concordantly exactly 1 time 689s 0 (0.00%) aligned concordantly >1 times 689s ---- 689s 48 pairs aligned concordantly 0 times; of these: 689s 0 (0.00%) aligned discordantly 1 time 689s ---- 689s 48 pairs aligned 0 times concordantly or discordantly; of these: 689s 96 mates make up the pairs; of these: 689s 96 (100.00%) aligned 0 times 689s 0 (0.00%) aligned exactly 1 time 689s 0 (0.00%) aligned >1 times 689s 0.00% overall alignment rate 689s Read 50 alignments... 689s Read 100 alignments... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s /usr/bin/bowtie2 --cp-min 5 --large-index --cp-ival 2 --local --mp 8.23022594701928,7.28389115032309 --gbar 1 --score-min L,8.07461839790576,4.45669908347513 --rfg 2.64059455154954 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s --- Summary --- 689s Read 1 reference strings 689s Checked 0 alignments, 0 edits 689s --------------- 689s PASSED 689s ALSO checking that bowtie2 and bowtie2-align match up 689s Warning: skipping mate #2 of read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #2 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 689s 48 reads; of these: 689s 48 (100.00%) were paired; of these: 689s 48 (100.00%) aligned concordantly 0 times 689s 0 (0.00%) aligned concordantly exactly 1 time 689s 0 (0.00%) aligned concordantly >1 times 689s ---- 689s 48 pairs aligned concordantly 0 times; of these: 689s 0 (0.00%) aligned discordantly 1 time 689s ---- 689s 48 pairs aligned 0 times concordantly or discordantly; of these: 689s 96 mates make up the pairs; of these: 689s 96 (100.00%) aligned 0 times 689s 0 (0.00%) aligned exactly 1 time 689s 0 (0.00%) aligned >1 times 689s 0.00% overall alignment rate 689s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 689s /usr/bin/bowtie2 --cp-min 5 --large-index --cp-ival 2 --local --mp 8.23022594701928,7.28389115032309 --gbar 1 --score-min L,8.07461839790576,4.45669908347513 --rfg 2.64059455154954 --qseq -p 2 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 689s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 689s Warning: skipping mate #2 of read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 689s Warning: skipping mate #2 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 689s 48 reads; of these: 689s 48 (100.00%) were paired; of these: 689s 48 (100.00%) aligned concordantly 0 times 689s 0 (0.00%) aligned concordantly exactly 1 time 689s 0 (0.00%) aligned concordantly >1 times 689s ---- 689s 48 pairs aligned concordantly 0 times; of these: 689s 0 (0.00%) aligned discordantly 1 time 689s ---- 689s 48 pairs aligned 0 times concordantly or discordantly; of these: 689s 96 mates make up the pairs; of these: 689s 96 (100.00%) aligned 0 times 689s 0 (0.00%) aligned exactly 1 time 689s 0 (0.00%) aligned >1 times 689s 0.00% overall alignment rate 689s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 689s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 689s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 689s Flattened IUPAC characters 689s Mutating sequence Sim.pm.2 689s Introducing 8 SNPs, 3/1 ref/read gaps, and 0 rearrangements 689s Finished SNPs 689s Finished ref gaps 689s Finished read gaps 689s Mutating sequence Sim.pm.1 689s *** Run 25 of 100 689s /usr/bin/bowtie2 --n-ceil 0.0907908544024558,1.41015384060474 --trim5 6 --cp-min 3 --large-index -a --cp-ival 2 --local -R 3 --score-min L,3.46442043337772,1.97978334002271 --mm -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 689s Introducing 8 SNPs, 0/3 ref/read gaps, and 0 rearrangements 689s Finished SNPs 689s Finished ref gaps 689s Finished read gaps 689s Mutated reference genome to subject genome 689s SNPs introduced: 16 689s Reference gaps introduced: 3 689s Read gaps introduced: 4 689s Rearrangements introduced: 0 689s Created read sampler 689s Sampling 120 reads 689s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 689s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 689s parsing sequence Sim.pm.1... 689s parsing sequence Sim.pm.2... 689s Parsed 234 reference bases 689s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '3' because it was < 2 characters long 689s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '4' because it was < 2 characters long 689s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '7' because it was < 2 characters long 689s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '10' because it was < 2 characters long 689s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 689s Warning: skipping read '12' because it was < 2 characters long 689s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '15' because it was < 2 characters long 689s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '23' because it was < 2 characters long 689s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '33' because it was < 2 characters long 689s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 689s Warning: skipping read '34' because it was < 2 characters long 689s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '35' because it was < 2 characters long 689s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '40' because it was < 2 characters long 689s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '45' because it was < 2 characters long 689s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '48' because it was < 2 characters long 689s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '52' because it was < 2 characters long 689s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '54' because it was < 2 characters long 689s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '61' because it was < 2 characters long 689s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '71' because it was < 2 characters long 689s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '79' because it was < 2 characters long 689s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '80' because it was < 2 characters long 689s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 689s Warning: skipping read '81' because it was < 2 characters long 689s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '82' because it was < 2 characters long 689s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '84' because it was < 2 characters long 689s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 689s Warning: skipping read '92' because it was < 2 characters long 689s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '101' because it was < 2 characters long 689s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '104' because it was < 2 characters long 689s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '105' because it was < 2 characters long 689s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '106' because it was < 2 characters long 689s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '109' because it was < 2 characters long 689s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 689s Warning: skipping read '116' because it was < 2 characters long 689s 120 reads; of these: 689s 120 (100.00%) were unpaired; of these: 689s 120 (100.00%) aligned 0 times 689s 0 (0.00%) aligned exactly 1 time 689s 0 (0.00%) aligned >1 times 689s 0.00% overall alignment rate 689s Read 50 alignments... 689s Read 100 alignments... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s --- Summary --- 689s Read 1 reference strings 689s Checked 0 alignments, 0 edits 689s --------------- 689s PASSED 689s Flattened IUPAC characters 689s Mutating sequence Sim.pm.1 689s Introducing 0 SNPs, 2/0 ref/read gaps, and 0 rearrangements 689s Finished SNPs 689s Finished ref gaps 689s Finished read gaps 689s Mutating sequence Sim.pm.2 689s Introducing 11 SNPs, 2/1 ref/read gaps, and 1 rearrangements 689s Finished SNPs 689s Finished ref gaps 689s Finished read gaps 689s Mutated reference genome to subject genome 689s SNPs introduced: 11 689s Reference gaps introduced: 4 689s Read gaps introduced: 1 689s Rearrangements introduced: 1 689s Created read sampler 689s Sampling 44 reads 689s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 689s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 689s parsing sequence Sim.pm.1... 689s parsing sequence Sim.pm.2... 689s Parsed 234 reference bases 689s *** Run 26 of 100 689s /usr/bin/bowtie2 --cp-ival 1 --local --cp-min 2 --np 1 --large-index --mm --rdg 4.9014180985375,17.4388285625262 --mp 8.72450138189952,3.64556619658746 -D 33 --score-min L,7.89267375128217,7.66912010771931 -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw 689s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 689s Warning: skipping read '18' because it was < 2 characters long 689s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 689s Warning: skipping read '19' because it was < 2 characters long 689s 44 reads; of these: 689s 44 (100.00%) were unpaired; of these: 689s 44 (100.00%) aligned 0 times 689s 0 (0.00%) aligned exactly 1 time 689s 0 (0.00%) aligned >1 times 689s 0.00% overall alignment rate 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s Processing line... 689s --- Summary --- 689s Read 1 reference strings 689s Checked 0 alignments, 0 edits 689s --------------- 689s PASSED 689s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 689s /usr/bin/bowtie2 --cp-ival 1 --local --cp-min 2 --np 1 --large-index --mm --rdg 4.9014180985375,17.4388285625262 --mp 8.72450138189952,3.64556619658746 -D 33 --score-min L,7.89267375128217,7.66912010771931 -r -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 689s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 689s Warning: skipping read '18' because it was < 2 characters long 689s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 689s Warning: skipping read '19' because it was < 2 characters long 690s 44 reads; of these: 690s 44 (100.00%) were unpaired; of these: 690s 44 (100.00%) aligned 0 times 690s 0 (0.00%) aligned exactly 1 time 690s 0 (0.00%) aligned >1 times 690s 0.00% overall alignment rate 690s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 690s Flattened IUPAC characters 690s Mutating sequence Sim.pm.2 690s Introducing 13 SNPs, 0/1 ref/read gaps, and 2 rearrangements 690s Finished SNPs 690s Finished ref gaps 690s Finished read gaps 690s Mutating sequence Sim.pm.1 690s Introducing 18 SNPs, 3/4 ref/read gaps, and 0 rearrangements 690s Finished SNPs 690s Finished ref gaps 690s Finished read gaps 690s Mutated reference genome to subject genome 690s SNPs introduced: 31 690s Reference gaps introduced: 3 690s Read gaps introduced: 5 690s Rearrangements introduced: 2 690s Created read sampler 690s Sampling 89 reads 690s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 690s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 690s *** Run 27 of 100 690s /usr/bin/bowtie2 --rdg 45.9231720815737 --score-min L,7.74014713005745,4.09508707378172 --cp-min 9 --large-index --rfg 11.1755849974811 -N 1 -L22 --local --cp-ival 1 -M 3 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 690s parsing sequence Sim.pm.1... 690s parsing sequence Sim.pm.2... 690s Parsed 234 reference bases 690s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 690s Warning: skipping mate #2 of read '1' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #2 of read '1' because it was < 2 characters long 690s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #2 of read '19' because it was < 2 characters long 690s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read '24' because it was < 2 characters long 690s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #2 of read '41' because it was < 2 characters long 690s Warning: skipping mate #1 of read '59' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read '59' because it was < 2 characters long 690s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #2 of read '77' because it was < 2 characters long 690s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read '82' because it was < 2 characters long 690s Read 50 alignments... 690s 89 reads; of these: 690s 89 (100.00%) were paired; of these: 690s 89 (100.00%) aligned concordantly 0 times 690s 0 (0.00%) aligned concordantly exactly 1 time 690s 0 (0.00%) aligned concordantly >1 times 690s ---- 690s 89 pairs aligned concordantly 0 times; of these: 690s 0 (0.00%) aligned discordantly 1 time 690s ---- 690s 89 pairs aligned 0 times concordantly or discordantly; of these: 690s 178 mates make up the pairs; of these: 690s 178 (100.00%) aligned 0 times 690s 0 (0.00%) aligned exactly 1 time 690s 0 (0.00%) aligned >1 times 690s 0.00% overall alignment rate 690s Read 100 alignments... 690s Read 150 alignments... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s --- Summary --- 690s Read 1 reference strings 690s Checked 0 alignments, 0 edits 690s --------------- 690s PASSED 690s Flattened IUPAC characters 690s Mutating sequence Sim.pm.1 690s Introducing 16 SNPs, 2/0 ref/read gaps, and 0 rearrangements 690s Finished SNPs 690s Finished ref gaps 690s Finished read gaps 690s Mutating sequence Sim.pm.2 690s Introducing 10 SNPs, 0/2 ref/read gaps, and 1 rearrangements 690s Finished SNPs 690s Finished ref gaps 690s Finished read gaps 690s Mutated reference genome to subject genome 690s SNPs introduced: 26 690s Reference gaps introduced: 2 690s Read gaps introduced: 2 690s Rearrangements introduced: 1 690s Created read sampler 690s Sampling 89 reads 690s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 690s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 690s parsing sequence Sim.pm.1... 690s *** Run 28 of 100 690s /usr/bin/bowtie2 --cp-min 3 --large-index --trim5 4 --norc --cp-ival 1 --score-min L,4.63608061944454,5.80799662958817 -N 0 -L24 -D 39 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 690s parsing sequence Sim.pm.2... 690s Parsed 234 reference bases 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 690s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '17' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 690s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '24' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 690s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '32' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 690s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 690s Warning: skipping read '36' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 690s Read 50 alignments... 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 690s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '51' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 690s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '57' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 690s Warning: skipping mate #1 of read '58' because length (1) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '58' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 690s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 690s Warning: skipping read '65' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 690s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '83' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 690s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '85' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 690s 89 reads; of these: 690s 81 (91.01%) were paired; of these: 690s 80 (98.77%) aligned concordantly 0 times 690s 0 (0.00%) aligned concordantly exactly 1 time 690s 1 (1.23%) aligned concordantly >1 times 690s ---- 690s 80 pairs aligned concordantly 0 times; of these: 690s 0 (0.00%) aligned discordantly 1 time 690s ---- 690s 80 pairs aligned 0 times concordantly or discordantly; of these: 690s 160 mates make up the pairs; of these: 690s 141 (88.12%) aligned 0 times 690s 6 (3.75%) aligned exactly 1 time 690s 13 (8.12%) aligned >1 times 690s 8 (8.99%) were unpaired; of these: 690s 8 (100.00%) aligned 0 times 690s 0 (0.00%) aligned exactly 1 time 690s 0 (0.00%) aligned >1 times 690s 12.35% overall alignment rate 690s Read 100 alignments... 690s Read 150 alignments... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s CCC 690s CCC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GTGTCGTTGTAGGCC 690s GTGTCGTTGTAGGCC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GGTCT 690s GGTCT 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GATTCGGTTGGTTTATGTCA 690s GATTCGGTTGGTTTATGTCA 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GCCGTTCCCGGTGT 690s GCCGTTCCCGGTGT 690s Processing line... 690s Processing line... 690s GTG 690s GTG 690s Processing line... 690s TAG 690s TAG 690s Processing line... 690s CGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGT 690s CGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGT 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s AA 690s AA 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s CCG 690s CCG 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GTCC 690s GTCC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s TT 690s TT 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s CC 690s CC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GGC 690s GGC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GGCGGGGCCAGTTCGA 690s GGCGGGGCCAGTTCGA 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GGTGTGTCGTTG 690s GGTGTGTCGTTG 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GCC 690s GCC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s TGGGGTTCGCC 690s TGGGGTTCGCC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GGGCC 690s GGGCC 690s Processing line... 690s GTGTCGTT 690s GTGTCGTT 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s CGGTGTGTCGTTGTAGGCCGT 690s CGGTGTGTCGTTGTAGGCCGT 690s Processing line... 690s --- Summary --- 690s Read 1 reference strings 690s Checked 21 alignments, 0 edits 690s --------------- 690s PASSED 690s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 690s /usr/bin/bowtie2 --cp-min 3 --large-index --trim5 4 --norc --cp-ival 1 --score-min L,4.63608061944454,5.80799662958817 -N 0 -L24 -D 39 -q -p 4 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 690s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '17' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 690s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '24' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 690s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '32' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 690s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 690s Warning: skipping read '36' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 690s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 690s Warning: skipping read '65' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 690s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '51' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 690s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '57' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 690s Warning: skipping mate #1 of read '58' because length (1) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '58' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 690s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '83' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 690s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '85' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 690s 89 reads; of these: 690s 81 (91.01%) were paired; of these: 690s 80 (98.77%) aligned concordantly 0 times 690s 0 (0.00%) aligned concordantly exactly 1 time 690s 1 (1.23%) aligned concordantly >1 times 690s ---- 690s 80 pairs aligned concordantly 0 times; of these: 690s 0 (0.00%) aligned discordantly 1 time 690s ---- 690s 80 pairs aligned 0 times concordantly or discordantly; of these: 690s 160 mates make up the pairs; of these: 690s 141 (88.12%) aligned 0 times 690s 6 (3.75%) aligned exactly 1 time 690s 13 (8.12%) aligned >1 times 690s 8 (8.99%) were unpaired; of these: 690s 8 (100.00%) aligned 0 times 690s 0 (0.00%) aligned exactly 1 time 690s 0 (0.00%) aligned >1 times 690s 12.35% overall alignment rate 690s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 690s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 690s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 690s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 690s /usr/bin/bowtie2 --cp-min 3 --large-index --trim5 4 --norc --cp-ival 1 --score-min L,4.63608061944454,5.80799662958817 -N 0 -L24 -D 39 -q -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 690s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '17' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 690s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '24' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 690s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '32' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 690s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 690s Warning: skipping read '36' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 690s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '51' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 690s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '57' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 690s Warning: skipping mate #1 of read '58' because length (1) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '58' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 690s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 690s Warning: skipping read '65' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 690s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '83' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 690s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 690s Warning: skipping mate #1 of read '85' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 690s 89 reads; of these: 690s 81 (91.01%) were paired; of these: 690s 80 (98.77%) aligned concordantly 0 times 690s 0 (0.00%) aligned concordantly exactly 1 time 690s 1 (1.23%) aligned concordantly >1 times 690s ---- 690s 80 pairs aligned concordantly 0 times; of these: 690s 0 (0.00%) aligned discordantly 1 time 690s ---- 690s 80 pairs aligned 0 times concordantly or discordantly; of these: 690s 160 mates make up the pairs; of these: 690s 141 (88.12%) aligned 0 times 690s 6 (3.75%) aligned exactly 1 time 690s 13 (8.12%) aligned >1 times 690s 8 (8.99%) were unpaired; of these: 690s 8 (100.00%) aligned 0 times 690s 0 (0.00%) aligned exactly 1 time 690s 0 (0.00%) aligned >1 times 690s 12.35% overall alignment rate 690s Flattened IUPAC characters 690s Mutating sequence Sim.pm.2 690s Introducing 11 SNPs, 0/1 ref/read gaps, and 0 rearrangements 690s Finished SNPs 690s Finished ref gaps 690s Finished read gaps 690s Mutating sequence Sim.pm.1 690s Introducing 9 SNPs, 3/1 ref/read gaps, and 1 rearrangements 690s Finished SNPs 690s Finished ref gaps 690s Finished read gaps 690s Mutated reference genome to subject genome 690s SNPs introduced: 20 690s Reference gaps introduced: 3 690s Read gaps introduced: 2 690s Rearrangements introduced: 1 690s Created read sampler 690s Sampling 135 reads 690s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 690s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 690s parsing sequence Sim.pm.1... 690s parsing sequence Sim.pm.2... 690s Parsed 234 reference bases 690s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 690s *** Run 29 of 100 690s /usr/bin/bowtie2 --ma 35.0289480013124 --score-min L,1.0579289025273,9.53036332134199 --rdg 15.2710259393962,4.8799166678418 --np 1 --cp-min 10 --large-index -N 1 -L12 -i S,1.30857584449879,1.5974055020043 --trim3 6 --rfg 26.2835595440597,7.02726328341168 --trim5 3 -M 6 --cp-ival 1 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq 690s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 690s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 690s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 690s Warning: skipping mate #2 of read 'R_1_1_1_56_56_1/1' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #2 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 690s Read 50 alignments... 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 690s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 690s Read 100 alignments... 690s 135 reads; of these: 690s 115 (85.19%) were paired; of these: 690s 113 (98.26%) aligned concordantly 0 times 690s 0 (0.00%) aligned concordantly exactly 1 time 690s 2 (1.74%) aligned concordantly >1 times 690s ---- 690s 113 pairs aligned concordantly 0 times; of these: 690s 1 (0.88%) aligned discordantly 1 time 690s ---- 690s 112 pairs aligned 0 times concordantly or discordantly; of these: 690s 224 mates make up the pairs; of these: 690s 190 (84.82%) aligned 0 times 690s 14 (6.25%) aligned exactly 1 time 690s 20 (8.93%) aligned >1 times 690s 20 (14.81%) were unpaired; of these: 690s 16 (80.00%) aligned 0 times 690s 3 (15.00%) aligned exactly 1 time 690s 1 (5.00%) aligned >1 times 690s 17.60% overall alignment rate 690s Read 150 alignments... 690s Read 200 alignments... 690s Read 250 alignments... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s AGTTCGATTCGGTTGGTTTATGTCA 690s AGTTCGATTCGGTTGGTTTATGTCA 690s Processing line... 690s Processing line... 690s TAG 690s TAG 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GG 690s GG 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GTT 690s GTT 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GACG 690s GACG 690s Processing line... 690s Processing line... 690s TGGGTGCG 690s TGGGTGCG 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s TGTCGTTGT 690s TGTCGTTGT 690s Processing line... 690s Processing line... 690s CGT 690s CGT 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s TCGCCG 690s TCGCCG 690s Processing line... 690s Processing line... 690s CCGCGGCCCGT 690s CCGCGGCCCGT 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GGTAG 690s GGTAG 690s Processing line... 690s CGGCGGGGCCA 690s CGGCGGGGCCA 690s Processing line... 690s Processing line... 690s TCCCGG 690s TCCCGG 690s Processing line... 690s Processing line... 690s Processing line... 690s /usr/bin/bowtie2 --ma 35.0289480013124 --score-min L,1.0579289025273,9.53036332134199 --rdg 15.2710259393962,4.8799166678418 --np 1 --cp-min 10 --large-index -N 1 -L12 -i S,1.30857584449879,1.5974055020043 --trim3 6 --rfg 26.2835595440597,7.02726328341168 --trim5 3 -M 6 --cp-ival 1 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 690s Processing line... 690s Processing line... 690s GCC 690s GCC 690s Processing line... 690s CT 690s CT 690s Processing line... 690s TGACGCCGTTGAACGTGCGG 690s TGACGCCGTTGAACGTGCGG 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GCCGTTCCCGGTGTGTCGTTGTA 690s GCCGTTCCCGGTGTGTCGTTGTA 690s Processing line... 690s Processing line... 690s TTG 690s TTG 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s CAT 690s CAT 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GGG 690s GGG 690s Processing line... 690s Processing line... 690s GGGGCGTGGGTGCGGCGGGGCCAGTTC 690s GGGGCGTGGGTGCGGCGGGGCCAGTTC 690s Processing line... 690s CGTTCCCG 690s CGTTCCCG 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GGGCGTG 690s GGGCGTG 690s Processing line... 690s Processing line... 690s TC 690s TC 690s Processing line... 690s TCGC 690s TCGC 690s Processing line... 690s Processing line... 690s Processing line... 690s GCC 690s GCC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GCCGTTC 690s GCCGTTC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GTTGGAGTCCCGCGGCCC 690s GTTGGAGTCCCGCGGCCC 690s Processing line... 690s GGTGACGCCGTTGAACGTGCG 690s GGTGACGCCGTTGAACGTGCG 690s Processing line... 690s Processing line... 690s Processing line... 690s ACGTGCGGC 690s ACGTGCGGC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GTGACGCCGTTGAACGTGCGGC 690s GTGACGCCGTTGAACGTGCGGC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s GGCGGGGCCAGTTCG 690s GGCGGGGCCAGTTCG 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s CGCCGTTGAACGTG 690s CGCCGTTGAACGTG 690s Processing line... 690s Processing line... 690s GTGGGTGCGGC 690s GTGGGTGCGGC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s CGT 690s CGT 690s Processing line... 690s Processing line... 690s TCGC 690s TCGC 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s CGCCGTTCCCGGTGTGTCGTT 690s CGCCGTTCCCGGTGTGTCGTT 690s Processing line... 690s Processing line... 690s TCG 690s TCG 690s Processing line... 690s Processing line... 690s GACGCCGTTGAACGTGCGGCGGG 690s GACGCCGTTGAACGTGCGGCGGG 690s Processing line... 690s Processing line... 690s CG 690s CG 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s TCGATTCG 690s TCGATTCG 690s Processing line... 690s GTGCGG 690s GTGCGG 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s CAGGTTGGA 690s CAGGTTGGA 690s Processing line... 690s Processing line... 690s CGTTGAACG 690s CGTTGAACG 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s Processing line... 690s --- Summary --- 690s Read 1 reference strings 690s Checked 44 alignments, 0 edits 690s --------------- 690s PASSED 690s ALSO checking that bowtie2 and bowtie2-align match up 690s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 690s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 690s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 690s Warning: skipping mate #2 of read 'R_1_1_1_56_56_1/1' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #2 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 690s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 690s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (1) 690s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 690s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 690s 135 reads; of these: 690s 115 (85.19%) were paired; of these: 690s 113 (98.26%) aligned concordantly 0 times 690s 0 (0.00%) aligned concordantly exactly 1 time 690s 2 (1.74%) aligned concordantly >1 times 690s ---- 690s 113 pairs aligned concordantly 0 times; of these: 690s 1 (0.88%) aligned discordantly 1 time 690s ---- 690s 112 pairs aligned 0 times concordantly or discordantly; of these: 690s 224 mates make up the pairs; of these: 690s 190 (84.82%) aligned 0 times 690s 14 (6.25%) aligned exactly 1 time 690s 20 (8.93%) aligned >1 times 690s 20 (14.81%) were unpaired; of these: 690s 16 (80.00%) aligned 0 times 690s 3 (15.00%) aligned exactly 1 time 690s 1 (5.00%) aligned >1 times 690s 17.60% overall alignment rate 690s Flattened IUPAC characters 690s Mutating sequence Sim.pm.2 690s Introducing 1 SNPs, 0/2 ref/read gaps, and 2 rearrangements 690s Finished SNPs 690s Finished ref gaps 690s Finished read gaps 690s Mutating sequence Sim.pm.1 690s Introducing 6 SNPs, 2/0 ref/read gaps, and 1 rearrangements 690s Finished SNPs 690s Finished ref gaps 690s Finished read gaps 690s Mutated reference genome to subject genome 690s SNPs introduced: 7 690s Reference gaps introduced: 2 690s Read gaps introduced: 2 690s Rearrangements introduced: 3 690s Created read sampler 690s Sampling 53 reads 690s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 690s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 690s parsing sequence Sim.pm.1... 690s parsing sequence Sim.pm.2... 690s Parsed 234 reference bases 690s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 690s *** Run 30 of 100 690s /usr/bin/bowtie2 --large-index --np 3 --cp-min 4 --mm --score-min L,7.29623728347019,9.64414700761088 --gbar 3 -D 12 --local --cp-ival 1 -M 6 --rfg 49.4348426116452 --trim3 1 --mp 6.46070612974466,4.12857016731448 -N 0 -L20 --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq 691s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 691s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 691s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 691s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 691s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 691s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 691s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 691s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 691s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 691s 53 reads; of these: 691s 53 (100.00%) were unpaired; of these: 691s 53 (100.00%) aligned 0 times 691s 0 (0.00%) aligned exactly 1 time 691s 0 (0.00%) aligned >1 times 691s 0.00% overall alignment rate 691s Read 50 alignments... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s /usr/bin/bowtie2 --large-index --np 3 --cp-min 4 --mm --score-min L,7.29623728347019,9.64414700761088 --gbar 3 -D 12 --local --cp-ival 1 -M 6 --rfg 49.4348426116452 --trim3 1 --mp 6.46070612974466,4.12857016731448 -N 0 -L20 --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s --- Summary --- 691s Read 1 reference strings 691s Checked 0 alignments, 0 edits 691s --------------- 691s PASSED 691s ALSO checking that bowtie2 and bowtie2-align match up 691s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 691s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 691s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 691s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 691s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 691s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 691s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 691s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 691s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 691s 53 reads; of these: 691s 53 (100.00%) were unpaired; of these: 691s 53 (100.00%) aligned 0 times 691s 0 (0.00%) aligned exactly 1 time 691s 0 (0.00%) aligned >1 times 691s 0.00% overall alignment rate 691s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 691s /usr/bin/bowtie2 --large-index --np 3 --cp-min 4 --mm --score-min L,7.29623728347019,9.64414700761088 --gbar 3 -D 12 --local --cp-ival 1 -M 6 --rfg 49.4348426116452 --trim3 1 --mp 6.46070612974466,4.12857016731448 -N 0 -L20 --qseq -p 2 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 691s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 691s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 691s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 691s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 691s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 691s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 691s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 691s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 691s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 691s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 691s 53 reads; of these: 691s 53 (100.00%) were unpaired; of these: 691s 53 (100.00%) aligned 0 times 691s 0 (0.00%) aligned exactly 1 time 691s 0 (sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 691s 0.00%) aligned >1 times 691s 0.00% overall alignment rate 691s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 691s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 691s Flattened IUPAC characters 691s Mutating sequence Sim.pm.1 691s Introducing 16 SNPs, 1/0 ref/read gaps, and 1 rearrangements 691s Finished SNPs 691s Finished ref gaps 691s Finished read gaps 691s Mutating sequence Sim.pm.2 691s Introducing 0 SNPs, 0/3 ref/read gaps, and 0 rearrangements 691s Finished SNPs 691s Finished ref gaps 691s Finished read gaps 691s Mutated reference genome to subject genome 691s SNPs introduced: 16 691s Reference gaps introduced: 1 691s Read gaps introduced: 3 691s Rearrangements introduced: 1 691s Created read sampler 691s Sampling 172 reads 691s *** Run 31 of 100 691s /usr/bin/bowtie2 --rfg 22.9314620723828,7.58706190059905 -a --trim5 3 --n-ceil 0.539393113389804,1.02166348804785 --local --cp-ival 1 --score-min L,1.65451086342029,9.22167027082386 --rdg 14.6237316238774,2.91501207639278 --mm --large-index --cp-min 8 --np 2 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 691s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 691s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 691s parsing sequence Sim.pm.1... 691s parsing sequence Sim.pm.2... 691s Parsed 234 reference bases 691s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '14' because it was < 2 characters long 691s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '19' because it was < 2 characters long 691s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '24' because it was < 2 characters long 691s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '29' because it was < 2 characters long 691s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '30' because it was < 2 characters long 691s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '33' because it was < 2 characters long 691s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '43' because it was < 2 characters long 691s Warning: skipping mate #2 of read '43' because it was < 2 characters long 691s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '45' because it was < 2 characters long 691s Warning: skipping mate #2 of read '70' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '70' because it was < 2 characters long 691s Read 50 alignments... 691s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '82' because it was < 2 characters long 691s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '87' because it was < 2 characters long 691s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '94' because it was < 2 characters long 691s Warning: skipping mate #1 of read '113' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '113' because it was < 2 characters long 691s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '138' because it was < 2 characters long 691s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '143' because it was < 2 characters long 691s Warning: skipping mate #2 of read '154' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '154' because it was < 2 characters long 691s Read 100 alignments... 691s Warning: skipping mate #2 of read '166' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '166' because it was < 2 characters long 691s Warning: skipping mate #2 of read '167' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '167' because it was < 2 characters long 691s Read 150 alignments... 691s 172 reads; of these: 691s 161 (93.60%) were paired; of these: 691s 161 (100.00%) aligned concordantly 0 times 691s 0 (0.00%) aligned concordantly exactly 1 time 691s 0 (0.00%) aligned concordantly >1 times 691s ---- 691s 161 pairs aligned concordantly 0 times; of these: 691s 0 (0.00%) aligned discordantly 1 time 691s ---- 691s 161 pairs aligned 0 times concordantly or discordantly; of these: 691s 322 mates make up the pairs; of these: 691s 322 (100.00%) aligned 0 times 691s 0 (0.00%) aligned exactly 1 time 691s 0 (0.00%) aligned >1 times 691s 11 (6.40%) were unpaired; of these: 691s 11 (100.00%) aligned 0 times 691s 0 (0.00%) aligned exactly 1 time 691s 0 (0.00%) aligned >1 times 691s 0.00% overall alignment rate 691s Read 200 alignments... 691s Read 250 alignments... 691s Read 300 alignments... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s 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Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s /usr/bin/bowtie2 --rfg 22.9314620723828,7.58706190059905 -a --trim5 3 --n-ceil 0.539393113389804,1.02166348804785 --local --cp-ival 1 --score-min L,1.65451086342029,9.22167027082386 --rdg 14.6237316238774,2.91501207639278 --mm --large-index --cp-min 8 --np 2 -r -p 4 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s --- Summary --- 691s Read 1 reference strings 691s Checked 0 alignments, 0 edits 691s --------------- 691s PASSED 691s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 691s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '14' because it was < 2 characters long 691s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '19' because it was < 2 characters long 691s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '24' because it was < 2 characters long 691s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '29' because it was < 2 characters long 691s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '30' because it was < 2 characters long 691s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '33' because it was < 2 characters long 691s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '43' because it was < 2 characters long 691s Warning: skipping mate #2 of read '43' because it was < 2 characters long 691s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '45' because it was < 2 characters long 691s Warning: skipping mate #2 of read '70' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '70' because it was < 2 characters long 691s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '82' because it was < 2 characters long 691s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '87' because it was < 2 characters long 691s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '94' because it was < 2 characters long 691s Warning: skipping mate #1 of read '113' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '113' because it was < 2 characters long 691s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '138' because it was < 2 characters long 691s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 691s Warning: skipping mate #1 of read '143' because it was < 2 characters long 691s Warning: skipping mate #2 of read '154' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '154' because it was < 2 characters long 691s Warning: skipping mate #2 of read '166' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '166' because it was < 2 characters long 691s Warning: skipping mate #2 of read '167' because length (1) <= # seed mismatches (0) 691s Warning: skipping mate #2 of read '167' because it was < 2 characters long 691s 172 reads; of these: 691s 161 (93.60%) were paired; of these: 691s 161 (100.00%) aligned concordantly 0 times 691s 0 (0.00%) aligned concordantly exactly 1 time 691s 0 (0.00%) aligned concordantly >1 times 691s ---- 691s 161 pairs aligned concordantly 0 times; of these: 691s 0 (0.00%) aligned discordantly 1 time 691s ---- 691s 161 pairs aligned 0 times concordantly or discordantly; of these: 691s 322 mates make up the pairs; of these: 691s 322 (100.00%) aligned 0 times 691s 0 (0.00%) aligned exactly 1 time 691s 0 (0.00%) aligned >1 times 691s 11 (6.40%) were unpaired; of these: 691s 11 (100.00%) aligned 0 times 691s 0 (0.00%) aligned exactly 1 time 691s 0 (0.00%) aligned >1 times 691s 0.00% overall alignment rate 691s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 691s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 691s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 691s Flattened IUPAC characters 691s Mutating sequence Sim.pm.1 691s Introducing 11 SNPs, 3/1 ref/read gaps, and 1 rearrangements 691s Finished SNPs 691s Finished ref gaps 691s Finished read gaps 691s Mutating sequence Sim.pm.2 691s Introducing 26 SNPs, 3/3 ref/read gaps, and 0 rearrangements 691s Finished SNPs 691s Finished ref gaps 691s Finished read gaps 691s Mutated reference genome to subject genome 691s SNPs introduced: 37 691s Reference gaps introduced: 6 691s Read gaps introduced: 4 691s Rearrangements introduced: 1 691s Created read sampler 691s Sampling 65 reads 691s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 691s *** Run 32 of 100 691s /usr/bin/bowtie2 --local --cp-ival 1 --trim5 3 --rfg 45.6032078695822 --mp 4.665442393889,3.63426418039596 --cp-min 7 --np 1 --large-index --mm --score-min L,5.96547283188682,3.33632383802325 -R 1 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 691s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 691s parsing sequence Sim.pm.1... 691s parsing sequence Sim.pm.2... 691s Parsed 234 reference bases 691s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '1' because it was < 2 characters long 691s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '10' because it was < 2 characters long 691s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '19' because it was < 2 characters long 691s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 691s Warning: skipping read '39' because it was < 2 characters long 691s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '55' because it was < 2 characters long 691s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '59' because it was < 2 characters long 691s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '61' because it was < 2 characters long 691s 65 reads; of these: 691s 65 (100.00%) were unpaired; of these: 691s 65 (100.00%) aligned 0 times 691s 0 (0.00%) aligned exactly 1 time 691s 0 (0.00%) aligned >1 times 691s 0.00% overall alignment rate 691s Read 50 alignments... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s Processing line... 691s --- Summary --- 691s Read 1 reference strings 691s Checked 0 alignments, 0 edits 691s --------------- 691s PASSED 691s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 691s /usr/bin/bowtie2 --local --cp-ival 1 --trim5 3 --rfg 45.6032078695822 --mp 4.665442393889,3.63426418039596 --cp-min 7 --np 1 --large-index --mm --score-min L,5.96547283188682,3.33632383802325 -R 1 -q -p 4 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 691s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '1' because it was < 2 characters long 691s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '10' because it was < 2 characters long 691s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '19' because it was < 2 characters long 691s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 691s Warning: skipping read '39' because it was < 2 characters long 691s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '55' because it was < 2 characters long 691s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '59' because it was < 2 characters long 691s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '61' because it was < 2 characters long 691s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 691s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 691s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 691s 65 reads; of these: 691s 65 (100.00%) were unpaired; of these: 691s 65 (100.00%) aligned 0 times 691s 0 (0.00%) aligned exactly 1 time 691s 0 (0.00%) aligned >1 times 691s 0.00% overall alignment rate 691s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 691s /usr/bin/bowtie2 --local --cp-ival 1 --trim5 3 --rfg 45.6032078695822 --mp 4.665442393889,3.63426418039596 --cp-min 7 --np 1 --large-index --mm --score-min L,5.96547283188682,3.33632383802325 -R 1 -q -p 3 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 691s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '1' because it was < 2 characters long 691s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '10' because it was < 2 characters long 691s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '19' because it was < 2 characters long 691s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 691s Warning: skipping read '39' because it was < 2 characters long 691s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '55' because it was < 2 characters long 691s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '59' because it was < 2 characters long 691s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 691s Warning: skipping read '61' because it was < 2 characters long 691s 65 reads; of these: 691s 65 (100.00%) were unpaired; of these: 691s 65 (100.00%) aligned 0 times 691s 0 (0.00%) aligned exactly 1 time 691s 0 (0.00%) aligned >1 times 691s 0.00% overall alignment rate 692s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 692s Flattened IUPAC characters 692s Mutating sequence Sim.pm.2 692s Introducing 8 SNPs, 1/0 ref/read gaps, and 1 rearrangements 692s Finished SNPs 692s Finished ref gaps 692s Finished read gaps 692s Mutating sequence Sim.pm.1 692s Introducing 0 SNPs, 1/2 ref/read gaps, and 0 rearrangements 692s Finished SNPs 692s Finished ref gaps 692s Finished read gaps 692s Mutated reference genome to subject genome 692s SNPs introduced: 8 692s Reference gaps introduced: 2 692s Read gaps introduced: 2 692s Rearrangements introduced: 1 692s Created read sampler 692s Sampling 94 reads 692s *** Run 33 of 100 692s /usr/bin/bowtie2 --np 2 --cp-min 3 --large-index --ma 38.2219278835058 --score-min L,2.96678050662221,4.28502435154611 -R 1 --gbar 2 --cp-ival 2 -M 4 --norc --trim3 9 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq 692s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 692s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 692s parsing sequence Sim.pm.1... 692s parsing sequence Sim.pm.2... 692s Parsed 234 reference bases 692s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 692s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 692s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 692s Warning: skipping mate #2 of read 'R_1_1_1_35_35_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping mate #2 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 692s Warning: skipping mate #2 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping mate #2 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 692s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 692s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 692s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 692s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 692s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 692s Read 50 alignments... 692s 94 reads; of these: 692s 75 (79.79%) were paired; of these: 692s 75 (100.00%) aligned concordantly 0 times 692s 0 (0.00%) aligned concordantly exactly 1 time 692s 0 (0.00%) aligned concordantly >1 times 692s ---- 692s 75 pairs aligned concordantly 0 times; of these: 692s 0 (0.00%) aligned discordantly 1 time 692s ---- 692s 75 pairs aligned 0 times concordantly or discordantly; of these: 692s 150 mates make up the pairs; of these: 692s 137 (91.33%) aligned 0 times 692s 2 (1.33%) aligned exactly 1 time 692s 11 (7.33%) aligned >1 times 692s 19 (20.21%) were unpaired; of these: 692s 17 (89.47%) aligned 0 times 692s 0 (0.00%) aligned exactly 1 time 692s 2 (10.53%) aligned >1 times 692s 8.88% overall alignment rate 692s Read 100 alignments... 692s Read 150 alignments... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s GTC 692s GTC 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s CT 692s CT 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s CCCGGT 692s CCCGGT 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s CCGTTCCCGGTGTGTCGTTGT 692s CCGTTCCCGGTGTGTCGTTGT 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s CCC 692s CCC 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s CCGTTCCCGGTGTGTCGTTGTA 692s CCGTTCCCGGTGTGTCGTTGTA 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s GGGTTCGCCGTTCCCGGT 692s GGGTTCGCCGTTCCCGGT 692s Processing line... 692s Processing line... 692s GGGTTCGCCGTTCCCGGTGTGTC 692s GGGTTCGCCGTTCCCGGTGTGTC 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s GTGGGTGCGGCGGG 692s GTGGGTGCGGCGGG 692s Processing line... 692s Processing line... 692s GT 692s GT 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s GGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCG 692s GGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCG 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s CCCGGT 692s CCCGGT 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s CC 692s CC 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s TCGT 692s TCGT 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s GGTGCGGC 692s GGTGCGGC 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s --- Summary --- 692s Read 1 reference strings 692s Checked 15 alignments, 0 edits 692s --------------- 692s PASSED 692s Flattened IUPAC characters 692s Mutating sequence Sim.pm.2 692s Introducing 15 SNPs, 1/0 ref/read gaps, and 3 rearrangements 692s Finished SNPs 692s Finished ref gaps 692s Finished read gaps 692s Mutating sequence Sim.pm.1 692s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 692s Finished SNPs 692s Finished ref gaps 692s Finished read gaps 692s Mutated reference genome to subject genome 692s SNPs introduced: 19 692s Reference gaps introduced: 1 692s Read gaps introduced: 0 692s Rearrangements introduced: 4 692s Created read sampler 692s Sampling 59 reads 692s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 692s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 692s parsing sequence Sim.pm.1... 692s parsing sequence Sim.pm.2... 692s *** Run 34 of 100 692s /usr/bin/bowtie2 --cp-ival 1 --local --cp-min 2 --large-index --rfg 37.755140435969,12.8283513395162 --mm --mp 5.51523276222627,1.06572432424248 -k 3 --score-min L,2.122096146633,5.60775704945407 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 692s Parsed 234 reference bases 692s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 692s Warning: skipping read '39' because it was < 2 characters long 692s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 692s Warning: skipping read '42' because it was < 2 characters long 692s 59 reads; of these: 692s 59 (100.00%) were unpaired; of these: 692s 59 (100.00%) aligned 0 times 692s 0 (0.00%) aligned exactly 1 time 692s 0 (0.00%) aligned >1 times 692s 0.00% overall alignment rate 692s Read 50 alignments... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s /usr/bin/bowtie2 --cp-ival 1 --local --cp-min 2 --large-index --rfg 37.755140435969,12.8283513395162 --mm --mp 5.51523276222627,1.06572432424248 -k 3 --score-min L,2.122096146633,5.60775704945407 -q -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s --- Summary --- 692s Read 1 reference strings 692s Checked 0 alignments, 0 edits 692s --------------- 692s PASSED 692s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 692s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 692s Warning: skipping read '39' because it was < 2 characters long 692s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 692s Warning: skipping read '42' because it was < 2 characters long 692s 59 reads; of these: 692s 59 (100.00%) were unpaired; of these: 692s 59 (100.00%) aligned 0 times 692s 0 (0.00%) aligned exactly 1 time 692s 0 (0.00%) aligned >1 times 692s 0.00% overall alignment rate 692s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 692s Flattened IUPAC characters 692s Mutating sequence Sim.pm.1 692s Introducing 5 SNPs, 1/1 ref/read gaps, and 0 rearrangements 692s Finished SNPs 692s Finished ref gaps 692s Finished read gaps 692s Mutating sequence Sim.pm.2 692s Introducing 9 SNPs, 2/3 ref/read gaps, and 0 rearrangements 692s Finished SNPs 692s Finished ref gaps 692s Finished read gaps 692s Mutated reference genome to subject genome 692s SNPs introduced: 14 692s Reference gaps introduced: 3 692s Read gaps introduced: 4 692s Rearrangements introduced: 0 692s Created read sampler 692s Sampling 189 reads 692s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 692s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 692s parsing sequence Sim.pm.1... 692s parsing sequence Sim.pm.2... 692s Parsed 234 reference bases 692s *** Run 35 of 100 692s /usr/bin/bowtie2 --large-index --cp-min 3 --np 5 --n-ceil 0.918485353035506,1.0765897985595 --local --cp-ival 1 --score-min L,6.97250201863361,2.0367958741857 --nofw --mp 7.02297500844713,5.83896094435439 --rdg 42.7857367991412 --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq 692s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_151_151_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 692s Read 50 alignments... 692s Warning: skipping read 'R_1_1_1_185_185_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_185_185_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_187_187_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_187_187_1/1' because it was < 2 characters long 692s Read 100 alignments... 692s 189 reads; of these: 692s 189 (100.00%) were unpaired; of these: 692s 189 (100.00%) aligned 0 times 692s 0 (0.00%) aligned exactly 1 time 692s 0 (0.00%) aligned >1 times 692s 0.00% overall alignment rate 692s Read 150 alignments... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s /usr/bin/bowtie2 --large-index --cp-min 3 --np 5 --n-ceil 0.918485353035506,1.0765897985595 --local --cp-ival 1 --score-min L,6.97250201863361,2.0367958741857 --nofw --mp 7.02297500844713,5.83896094435439 --rdg 42.7857367991412 --qseq -p 4 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s --- Summary --- 692s Read 1 reference strings 692s Checked 0 alignments, 0 edits 692s --------------- 692s PASSED 692s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 692s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_151_151_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_185_185_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_185_185_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_187_187_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_187_187_1/1' because it was < 2 characters long 692s 189 reads; of these: 692s 189 (100.00%) were unpaired; of these: 692s 189 (100.00%) aligned 0 times 692s 0 (0.00%) aligned exactly 1 time 692s 0 (0.00%) aligned >1 times 692s 0.00% overall alignment rate 692s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 692s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 692s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 692s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 692s /usr/bin/bowtie2 --large-index --cp-min 3 --np 5 --n-ceil 0.918485353035506,1.0765897985595 --local --cp-ival 1 --score-min L,6.97250201863361,2.0367958741857 --nofw --mp 7.02297500844713,5.83896094435439 --rdg 42.7857367991412 --qseq -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 692s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_151_151_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_185_185_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_185_185_1/1' because it was < 2 characters long 692s Warning: skipping read 'R_1_1_1_187_187_1/1' because length (1) <= # seed mismatches (0) 692s Warning: skipping read 'R_1_1_1_187_187_1/1' because it was < 2 characters long 692s 189 reads; of these: 692s 189 (100.00%) were unpaired; of these: 692s 189 (100.00%) aligned 0 times 692s 0 (0.00%) aligned exactly 1 time 692s 0 (0.00%) aligned >1 times 692s 0.00% overall alignment rate 692s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 692s Flattened IUPAC characters 692s Mutating sequence Sim.pm.1 692s Introducing 20 SNPs, 3/2 ref/read gaps, and 1 rearrangements 692s Finished SNPs 692s Finished ref gaps 692s Finished read gaps 692s Mutating sequence Sim.pm.2 692s Introducing 6 SNPs, 0/2 ref/read gaps, and 0 rearrangements 692s Finished SNPs 692s Finished ref gaps 692s Finished read gaps 692s Mutated reference genome to subject genome 692s SNPs introduced: 26 692s Reference gaps introduced: 3 692s Read gaps introduced: 4 692s Rearrangements introduced: 1 692s Created read sampler 692s Sampling 13 reads 692s *** Run 36 of 100 692s /usr/bin/bowtie2 --trim5 4 --cp-min 3 --np 1 --large-index --cp-ival 1 --local -i C,0.747685203586352 --mp 9.66060759925826,9.51065124264237 --score-min L,7.22148187310713,1.92682546366945 --mm -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw 692s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 692s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 692s parsing sequence Sim.pm.1... 692s parsing sequence Sim.pm.2... 692s Parsed 234 reference bases 692s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 692s Warning: skipping read '9' because it was < 2 characters long 692s 13 reads; of these: 692s 13 (100.00%) were unpaired; of these: 692s 13 (100.00%) aligned 0 times 692s 0 (0.00%) aligned exactly 1 time 692s 0 (0.00%) aligned >1 times 692s 0.00% overall alignment rate 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s Processing line... 692s --- Summary --- 692s Read 1 reference strings 692s Checked 0 alignments, 0 edits 692s --------------- 692s PASSED 692s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 692s /usr/bin/bowtie2 --trim5 4 --cp-min 3 --np 1 --large-index --cp-ival 1 --local -i C,0.747685203586352 --mp 9.66060759925826,9.51065124264237 --score-min L,7.22148187310713,1.92682546366945 --mm -r -p 4 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 693s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 693s Warning: skipping read '9' because it was < 2 characters long 693s 13 reads; of these: 693s 13 (100.00%) were unpaired; of these: 693s 13 (100.00%) aligned 0 times 693s 0 (0.00%) aligned exactly 1 time 693s 0 (0.00%) aligned >1 times 693s 0.00% overall alignment rate 693s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 693s Flattened IUPAC characters 693s Mutating sequence Sim.pm.1 693s Introducing 16 SNPs, 1/0 ref/read gaps, and 4 rearrangements 693s Finished SNPs 693s Finished ref gaps 693s Finished read gaps 693s Mutating sequence Sim.pm.2 693s Introducing 4 SNPs, 0/2 ref/read gaps, and 0 rearrangements 693s Finished SNPs 693s Finished ref gaps 693s Finished read gaps 693s *** Run 37 of 100 693s /usr/bin/bowtie2 --local --cp-ival 1 --cp-min 6 --large-index --n-ceil 1.2176966287681,0.620929355164522 --trim5 7 --nofw --score-min L,2.88722883696409,6.41274347812086 -N 1 -L23 --mp 7.1394615149378,1.01095586034062 -k 4 --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq 693s /usr/bin/bowtie2 --local --cp-ival 1 --cp-min 6 --large-index --n-ceil 1.2176966287681,0.620929355164522 --trim5 7 --nofw --score-min L,2.88722883696409,6.41274347812086 -N 1 -L23 --mp 7.1394615149378,1.01095586034062 -k 4 --qseq -p 3 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 693s Mutated reference genome to subject genome 693s SNPs introduced: 20 693s Reference gaps introduced: 1 693s Read gaps introduced: 2 693s Rearrangements introduced: 4 693s Created read sampler 693s Sampling 46 reads 693s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 693s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 693s parsing sequence Sim.pm.1... 693s parsing sequence Sim.pm.2... 693s Parsed 234 reference bases 693s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 693s 46 reads; of these: 693s 46 (100.00%) were unpaired; of these: 693s 46 (100.00%) aligned 0 times 693s 0 (0.00%) aligned exactly 1 time 693s 0 (0.00%) aligned >1 times 693s 0.00% overall alignment rate 693s Read 50 alignments... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s --- Summary --- 693s Read 1 reference strings 693s Checked 0 alignments, 0 edits 693s --------------- 693s PASSED 693s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 693s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (1) 693s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 693s 46 reads; of these: 693s 46 (100.00%) were unpaired; of these: 693s 46 (100.00%) aligned 0 times 693s 0 (0.00%) aligned exactly 1 time 693s 0 (0.00%) aligned >1 times 693s 0.00% overall alignment rate 693s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 693s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 693s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 693s Flattened IUPAC characters 693s Mutating sequence Sim.pm.2 693s Introducing 10 SNPs, 4/0 ref/read gaps, and 0 rearrangements 693s Finished SNPs 693s Finished ref gaps 693s Finished read gaps 693s Mutating sequence Sim.pm.1 693s Introducing 21 SNPs, 0/0 ref/read gaps, and 0 rearrangements 693s Finished SNPs 693s Finished ref gaps 693s Finished read gaps 693s Mutated reference genome to subject genome 693s SNPs introduced: 31 693s Reference gaps introduced: 4 693s Read gaps introduced: 0 693s Rearrangements introduced: 0 693s Created read sampler 693s Sampling 163 reads 693s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 693s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 693s *** Run 38 of 100 693s /usr/bin/bowtie2 --gbar 3 -i S,0.30195702177768,3.26539584461537 --mp 5.14252090366291,4.74245639616102 --score-min L,8.81037132622747,3.87928409676028 --trim3 5 --rdg 41.5789768054211,6.27893790635733 --norc --large-index --cp-min 2 --cp-ival 1 --local --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq 693s parsing sequence Sim.pm.1... 693s parsing sequence Sim.pm.2... 693s Parsed 234 reference bases 693s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (1) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_118_118_1/1' because length (1) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 693s Read 50 alignments... 693s 163 reads; of these: 693s 163 (100.00%) were unpaired; of these: 693s 163 (100.00%) aligned 0 times 693s 0 (0.00%) aligned exactly 1 time 693s 0 (0.00%) aligned >1 times 693s 0.00% overall alignment rate 693s Read 100 alignments... 693s Read 150 alignments... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s /usr/bin/bowtie2 --gbar 3 -i S,0.30195702177768,3.26539584461537 --mp 5.14252090366291,4.74245639616102 --score-min L,8.81037132622747,3.87928409676028 --trim3 5 --rdg 41.5789768054211,6.27893790635733 --norc --large-index --cp-min 2 --cp-ival 1 --local --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s --- Summary --- 693s Read 1 reference strings 693s Checked 0 alignments, 0 edits 693s --------------- 693s PASSED 693s ALSO checking that bowtie2 and bowtie2-align match up 693s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (1) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_118_118_1/1' because length (1) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 693s Warning: skipping read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 693s Warning: skipping read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 693s 163 reads; of these: 693s 163 (100.00%) were unpaired; of these: 693s 163 (100.00%) aligned 0 times 693s 0 (0.00%) aligned exactly 1 time 693s 0 (0.00%) aligned >1 times 693s 0.00% overall alignment rate 693s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 693s Flattened IUPAC characters 693s Mutating sequence Sim.pm.1 693s Introducing 14 SNPs, 0/0 ref/read gaps, and 3 rearrangements 693s Finished SNPs 693s Finished ref gaps 693s Finished read gaps 693s Mutating sequence Sim.pm.2 693s Introducing 7 SNPs, 0/0 ref/read gaps, and 4 rearrangements 693s Finished SNPs 693s Finished ref gaps 693s Finished read gaps 693s Mutated reference genome to subject genome 693s SNPs introduced: 21 693s Reference gaps introduced: 0 693s Read gaps introduced: 0 693s Rearrangements introduced: 7 693s Created read sampler 693s Sampling 96 reads 693s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 693s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 693s parsing sequence Sim.pm.1... 693s parsing sequence Sim.pm.2... 693s Parsed 234 reference bases 693s *** Run 39 of 100 693s /usr/bin/bowtie2 --rdg 15.1052497643727,14.3296420308852 -D 23 --mp 5.31936768495769,3.26124568665674 --score-min L,2.84181096058056,4.82996873676188 --cp-ival 3 --large-index --cp-min 3 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 693s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #2 of read '30' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 693s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #1 of read '42' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 693s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #2 of read '61' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 693s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #1 of read '65' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 693s Warning: skipping mate #1 of read '79' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #1 of read '79' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 693s Read 50 alignments... 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 693s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #2 of read '91' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 693s 96 reads; of these: 693s 96 (100.00%) were paired; of these: 693s 95 (98.96%) aligned concordantly 0 times 693s 0 (0.00%) aligned concordantly exactly 1 time 693s 1 (1.04%) aligned concordantly >1 times 693s ---- 693s 95 pairs aligned concordantly 0 times; of these: 693s 2 (2.11%) aligned discordantly 1 time 693s ---- 693s 93 pairs aligned 0 times concordantly or discordantly; of these: 693s 186 mates make up the pairs; of these: 693s 164 (88.17%) aligned 0 times 693s 10 (5.38%) aligned exactly 1 time 693s 12 (6.45%) aligned >1 times 693s 14.58% overall alignment rate 693s Read 100 alignments... 693s Read 150 alignments... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s GG 693s GG 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s GCGGT 693s GCGGT 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s TCGTTGTAGGCCGTTGGGGTTCGCCG 693s TCGTTGTAGGCCGTTGGGGTTCGCCG 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s GTT 693s GTT 693s Processing line... 693s TTGGGGTTCGCCGTTCCC 693s TTGGGGTTCGCCGTTCCC 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s GAG 693s GAG 693s Processing line... 693s GCCCGT 693s GCCCGT 693s Processing line... 693s TTCGGTTGGTT 693s TTCGGTTGGTT 693s Processing line... 693s Processing line... 693s CCGTTCCCGGTGTGTCGTTGTAG 693s CCGTTCCCGGTGTGTCGTTGTAG 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s GGGTTCG 693s GGGTTCG 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s GTCTCAGG 693s GTCTCAGG 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s TTCGCCGTTCCCGG 693s TTCGCCGTTCCCGG 693s Processing line... 693s Processing line... 693s /usr/bin/bowtie2 --rdg 15.1052497643727,14.3296420308852 -D 23 --mp 5.31936768495769,3.26124568665674 --score-min L,2.84181096058056,4.82996873676188 --cp-ival 3 --large-index --cp-min 3 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 693s Processing line... 693s Processing line... 693s CGGTTGGTTTATGTCATCGCGCGGT 693s CGGTTGGTTTATGTCATCGCGCGGT 693s Processing line... 693s Processing line... 693s GGCGTGGG 693s GGCGTGGG 693s Processing line... 693s GCGGCGGGGCCAGTTCGATTCGGTTGGTT 693s GCGGCGGGGCCAGTTCGATTCGGTTGGTT 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s CGGGGCCAGTT 693s CGGGGCCAGTT 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s TGGTGACGCCG 693s TGGTGACGCCG 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s CGATT 693s CGATT 693s Processing line... 693s Processing line... 693s CGATTCGGTTG 693s CGATTCGGTTG 693s Processing line... 693s TTCGGTTGGTTTATGTC 693s TTCGGTTGGTTTATGTC 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s GTGTCGTTGTAGGCCGTTGGG 693s GTGTCGTTGTAGGCCGTTGGG 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s GCGGCGG 693s GCGGCGG 693s Processing line... 693s Processing line... 693s CTGGTGACGCCGTTGAACGT 693s CTGGTGACGCCGTTGAACGT 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s TCGTT 693s TCGTT 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s TT 693s TT 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s GTCGTTGTAGGCC 693s GTCGTTGTAGGCC 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s Processing line... 693s TTCGATTCGGTTGGTTTATGTCATCGCGCG 693s TTCGATTCGGTTGGTTTATGTCATCGCGCG 693s Processing line... 693s CC 693s CC 693s --- Summary --- 693s Read 1 reference strings 693s Checked 28 alignments, 0 edits 693s --------------- 693s PASSED 693s ALSO checking that bowtie2 and bowtie2-align match up 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 693s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #2 of read '30' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 693s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #1 of read '42' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 693s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #2 of read '61' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 693s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #1 of read '65' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 693s Warning: skipping mate #1 of read '79' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #1 of read '79' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 693s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #2 of read '91' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 693s 96 reads; of these: 693s 96 (100.00%) were paired; of these: 693s 95 (98.96%) aligned concordantly 0 times 693s 0 (0.00%) aligned concordantly exactly 1 time 693s 1 (1.04%) aligned concordantly >1 times 693s ---- 693s 95 pairs aligned concordantly 0 times; of these: 693s 2 (2.11%) aligned discordantly 1 time 693s ---- 693s 93 pairs aligned 0 times concordantly or discordantly; of these: 693s 186 mates make up the pairs; of these: 693s 164 (88.17%) aligned 0 times 693s 10 (5.38%) aligned exactly 1 time 693s 12 (6.45%) aligned >1 times 693s 14.58% overall alignment rate 693s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 693s /usr/bin/bowtie2 --rdg 15.1052497643727,14.3296420308852 -D 23 --mp 5.31936768495769,3.26124568665674 --score-min L,2.84181096058056,4.82996873676188 --cp-ival 3 --large-index --cp-min 3 -r -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 693s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 693s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #2 of read '30' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 693s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #1 of read '42' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 693s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #2 of read '61' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 693s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #1 of read '65' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 693s Warning: skipping mate #1 of read '79' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #1 of read '79' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 693s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (0) 693s Warning: skipping mate #2 of read '91' because it was < 2 characters long 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 693s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 693s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 693s 96 reads; of these: 693s 96 (100.00%) were paired; of these: 693s 95 (98.96%) aligned concordantly 0 times 693s 0 (0.00%) aligned concordantly exactly 1 time 693s 1 (1.04%) aligned concordantly >1 times 693s ---- 693s 95 pairs aligned concordantly 0 times; of these: 693s 2 (2.11%) aligned discordantly 1 time 693s ---- 693s 93 pairs aligned 0 times concordantly or discordantly; of these: 693s 186 mates make up the pairs; of these: 693s 164 (88.17%) aligned 0 times 693s 10 (5.38%) aligned exactly 1 time 693s 12 (6.45%) aligned >1 times 693s 14.58% overall alignment rate 693s Flattened IUPAC characters 693s *** Run 40 of 100 693s /usr/bin/bowtie2 --cp-ival 1 --norc -N 0 -L12 --mp 5.82284780356198,3.63646897305728 --trim3 4 --np 1 --cp-min 7 --large-index --gbar 1 -k 6 --ma 9.27705040553086 --score-min L,2.05108678915649,6.78005976709774 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 693s Mutating sequence Sim.pm.2 693s Introducing 18 SNPs, 0/0 ref/read gaps, and 0 rearrangements 693s Finished SNPs 693s Finished ref gaps 693s Finished read gaps 693s Mutating sequence Sim.pm.1 693s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 693s Finished SNPs 693s Finished ref gaps 693s Finished read gaps 693s Mutated reference genome to subject genome 693s SNPs introduced: 22 693s Reference gaps introduced: 0 693s Read gaps introduced: 0 693s Rearrangements introduced: 1 693s Created read sampler 693s Sampling 73 reads 693s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 693s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 693s parsing sequence Sim.pm.1... 693s parsing sequence Sim.pm.2... 693s Parsed 234 reference bases 694s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 694s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '1' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 694s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '3' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 694s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '9' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 694s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '14' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 694s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '16' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 694s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '20' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 694s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '24' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 694s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '37' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 694s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '41' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 694s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '46' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 694s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '55' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 694s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '56' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 694s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '58' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 694s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '73' because it was < 2 characters long 694s Read 50 alignments... 694s Read 100 alignments... 694s 73 reads; of these: 694s 64 (87.67%) were paired; of these: 694s 64 (100.00%) aligned concordantly 0 times 694s 0 (0.00%) aligned concordantly exactly 1 time 694s 0 (0.00%) aligned concordantly >1 times 694s ---- 694s 64 pairs aligned concordantly 0 times; of these: 694s 1 (1.56%) aligned discordantly 1 time 694s ---- 694s 63 pairs aligned 0 times concordantly or discordantly; of these: 694s 126 mates make up the pairs; of these: 694s 109 (86.51%) aligned 0 times 694s 5 (3.97%) aligned exactly 1 time 694s 12 (9.52%) aligned >1 times 694s 9 (12.33%) were unpaired; of these: 694s 9 (100.00%) aligned 0 times 694s 0 (0.00%) aligned exactly 1 time 694s 0 (0.00%) aligned >1 times 694s 13.87% overall alignment rate 694s Read 150 alignments... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GCCGTTGAACGTG 694s GCCGTTGAACGTG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTC 694s TTC 694s Processing line... 694s TTC 694s TTC 694s Processing line... 694s TTC 694s TTC 694s Processing line... 694s TTC 694s TTC 694s Processing line... 694s TTC 694s TTC 694s Processing line... 694s TTC 694s TTC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CGCC 694s CGCC 694s Processing line... 694s CGCC 694s CGCC 694s Processing line... 694s CGCC 694s CGCC 694s Processing line... 694s Processing line... 694s GGGCC 694s GGGCC 694s Processing line... 694s GGGCC 694s GGGCC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GTCATCGC 694s GTCATCGC 694s Processing line... 694s TTCGGTTG 694s TTCGGTTG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTGTAGGCCGTTGGGGTTCGCCGTTCC 694s TTGTAGGCCGTTGGGGTTCGCCGTTCC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CCG 694s CCG 694s Processing line... 694s CCG 694s CCG 694s Processing line... 694s CCG 694s CCG 694s Processing line... 694s CCG 694s CCG 694s Processing line... 694s CCG 694s CCG 694s Processing line... 694s CCG 694s CCG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GG 694s GG 694s Processing line... 694s GG 694s GG 694s Processing line... 694s GG 694s GG 694s Processing line... 694s GG 694s GG 694s Processing line... 694s GG 694s GG 694s Processing line... 694s GG 694s GG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGTGTGTCGTTGTAGG 694s GGTGTGTCGTTGTAGG 694s Processing line... 694s GGTGTGTCGTTGTAGG 694s GGTGTGTCGTTGTAGG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GCGTG 694s GCGTG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTCGCCGT 694s TTCGCCGT 694s Processing line... 694s TTCGCCGT 694s TTCGCCGT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GAGTCCCGCGGCCCGT 694s GAGTCCCGCGGCCCGT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CC 694s CC 694s Processing line... 694s CC 694s CC 694s Processing line... 694s CC 694s CC 694s Processing line... 694s CC 694s CC 694s Processing line... 694s CC 694s CC 694s Processing line... 694s CC 694s CC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TCGCCGTTCCCG 694s TCGCCGTTCCCG 694s Processing line... 694s TCGCCGTTCCCG 694s TCGCCGTTCCCG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GTTGAACG 694s GTTGAACG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTCCCGGTGTGTCGTTG 694s TTCCCGGTGTGTCGTTG 694s Processing line... 694s TTCCCGGTGTGTCGTTG 694s TTCCCGGTGTGTCGTTG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTCGCCGTTCCCGGTGT 694s TTCGCCGTTCCCGGTGT 694s Processing line... 694s TTCGCCGTTCCCGGTGT 694s TTCGCCGTTCCCGGTGT 694s Processing line... 694s Processing line... 694s GCCA 694s GCCA 694s /usr/bin/bowtie2 --cp-ival 1 --norc -N 0 -L12 --mp 5.82284780356198,3.63646897305728 --trim3 4 --np 1 --cp-min 7 --large-index --gbar 1 -k 6 --ma 9.27705040553086 --score-min L,2.05108678915649,6.78005976709774 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 694s Processing line... 694s GCCA 694s GCCA 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s --- Summary --- 694s Read 1 reference strings 694s Checked 48 alignments, 0 edits 694s --------------- 694s PASSED 694s ALSO checking that bowtie2 and bowtie2-align match up 694s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 694s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '1' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 694s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '3' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 694s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '9' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 694s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '14' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 694s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '16' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 694s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '20' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 694s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '24' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 694s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '37' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 694s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '41' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 694s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '46' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 694s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '55' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 694s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '56' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 694s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '58' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 694s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '73' because it was < 2 characters long 694s 73 reads; of these: 694s 64 (87.67%) were paired; of these: 694s 64 (100.00%) aligned concordantly 0 times 694s 0 (0.00%) aligned concordantly exactly 1 time 694s 0 (0.00%) aligned concordantly >1 times 694s ---- 694s 64 pairs aligned concordantly 0 times; of these: 694s 1 (1.56%) aligned discordantly 1 time 694s ---- 694s 63 pairs aligned 0 times concordantly or discordantly; of these: 694s 126 mates make up the pairs; of these: 694s 109 (86.51%) aligned 0 times 694s 5 (3.97%) aligned exactly 1 time 694s 12 (9.52%) aligned >1 times 694s 9 (12.33%) were unpaired; of these: 694s 9 (100.00%) aligned 0 times 694s 0 (0.00%) aligned exactly 1 time 694s 0 (0.00%) aligned >1 times 694s 13.87% overall alignment rate 694s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 694s /usr/bin/bowtie2 --cp-ival 1 --norc -N 0 -L12 --mp 5.82284780356198,3.63646897305728 --trim3 4 --np 1 --cp-min 7 --large-index --gbar 1 -k 6 --ma 9.27705040553086 --score-min L,2.05108678915649,6.78005976709774 -q -p 4 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 694s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 694s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 694s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '1' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 694s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '3' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 694s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '9' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 694s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '14' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 694s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '16' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 694s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '20' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 694s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '24' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 694s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '37' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 694s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '41' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 694s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '46' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 694s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '55' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 694s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '56' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 694s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '58' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 694s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '73' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 694s 73 reads; of these: 694s 64 (87.67%) were paired; of these: 694s 64 (100.00%) aligned concordantly 0 times 694s 0 (0.00%) aligned concordantly exactly 1 time 694s 0 (0.00%) aligned concordantly >1 times 694s ---- 694s 64 pairs aligned concordantly 0 times; of these: 694s 1 (1.56%) aligned discordantly 1 time 694s ---- 694s 63 pairs aligned 0 times concordantly or discordantly; of these: 694s 126 mates make up the pairs; of these: 694s 109 (86.51%) aligned 0 times 694s 5 (3.97%) aligned exactly 1 time 694s 12 (9.52%) aligned >1 times 694s 9 (12.33%) were unpaired; of these: 694s 9 (100.00%) aligned 0 times 694s 0 (0.00%) aligned exactly 1 time 694s 0 (0.00%) aligned >1 times 694s 13.87% overall alignment rate 694s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 694s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 694s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 694s Flattened IUPAC characters 694s Mutating sequence Sim.pm.2 694s Introducing 17 SNPs, 2/1 ref/read gaps, and 0 rearrangements 694s Finished SNPs 694s Finished ref gaps 694s Finished read gaps 694s Mutating sequence Sim.pm.1 694s Introducing 20 SNPs, 1/1 ref/read gaps, and 0 rearrangements 694s Finished SNPs 694s Finished ref gaps 694s Finished read gaps 694s Mutated reference genome to subject genome 694s SNPs introduced: 37 694s Reference gaps introduced: 3 694s Read gaps introduced: 2 694s Rearrangements introduced: 0 694s Created read sampler 694s Sampling 145 reads 694s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 694s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 694s parsing sequence Sim.pm.1... 694s parsing sequence Sim.pm.2... 694s Parsed 234 reference bases 694s *** Run 41 of 100 694s /usr/bin/bowtie2 --trim5 9 --large-index --np 1 --cp-min 6 --cp-ival 4 --mp 6.71713812507537,5.13528750534143 --score-min L,9.74381010337913,7.64719503885674 --rdg 36.3447113816163 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 694s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 694s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '3' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 694s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '4' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 694s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '5' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 694s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '8' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 694s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 694s Warning: skipping read '9' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 694s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '11' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 694s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '18' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 694s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '21' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 694s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '27' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 694s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '28' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 694s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '30' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 694s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '34' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 694s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '35' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 694s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '39' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 694s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '45' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 694s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '48' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 694s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 694s Warning: skipping read '56' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 694s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '59' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 694s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '61' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 694s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '62' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 694s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '66' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 694s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '67' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 694s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 694s Warning: skipping read '74' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 694s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '78' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 694s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '83' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 694s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '84' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 694s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '85' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 694s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '93' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 694s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '95' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 694s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '100' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 694s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '101' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 694s Warning: skipping read '105' because length (1) <= # seed mismatches (0) 694s Warning: skipping read '105' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 694s Warning: skipping read '111' because length (1) <= # seed mismatches (0) 694s Warning: skipping read '111' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 694s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '121' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 694s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '122' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 694s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '124' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 694s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '127' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 694s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '129' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 694s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '131' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 694s 145 reads; of these: 694s 145 (100.00%) were unpaired; of these: 694s 125 (86.21%) aligned 0 times 694s 9 (6.21%) aligned exactly 1 time 694s 11 (7.59%) aligned >1 times 694s 13.79% overall alignment rate 694s Read 50 alignments... 694s Read 100 alignments... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CAGGTTGGAGTCCC 694s CAGGTTGGAGTCCC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s AGGTTGGAGTCCCGCGGCC 694s AGGTTGGAGTCCCGCGGCC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGGGGCGTGGG 694s GGGGGCGTGGG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GTGTG 694s GTGTG 694s Processing line... 694s TCGATTCGGTTGGTTTATGTCATCGCGC 694s TCGATTCGGTTGGTTTATGTCATCGCGC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s AA 694s AA 694s Processing line... 694s Processing line... 694s TC 694s TC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTC 694s TTC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TAGGCCGTTGGGG 694s TAGGCCGTTGGGG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TCCCGGTGTG 694s TCCCGGTGTG 694s Processing line... 694s Processing line... 694s Processing line... 694s CGATTCGGTT 694s CGATTCGGTT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGCCCGT 694s GGCCCGT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGGGCGTG 694s GGGGCGTG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GTTGG 694s GTTGG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTGTAGGCCGTT 694s TTGTAGGCCGTT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTGGG 694s TTGGG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TCTCAGGTTGGA 694s TCTCAGGTTGGA 694s Processing line... 694s Processing line... 694s TCGGTTGGTT 694s TCGGTTGGTT 694s Processing line... 694s Processing line... 694s Processing line... 694s ACG 694s ACG 694s Processing line... 694s Processing line... 694s TGGGGTTCGCCGTTC 694s TGGGGTTCGCCGTTC 694s Processing line... 694s Processing line... 694s --- Summary --- 694s Read 1 reference strings 694s Checked 20 alignments, 0 edits 694s --------------- 694s PASSED 694s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 694s /usr/bin/bowtie2 --trim5 9 --large-index --np 1 --cp-min 6 --cp-ival 4 --mp 6.71713812507537,5.13528750534143 --score-min L,9.74381010337913,7.64719503885674 --rdg 36.3447113816163 -q -p 4 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 694s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 694s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '3' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 694s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '4' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 694s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '5' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 694s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '8' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 694s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 694s Warning: skipping read '9' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 694s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '11' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 694s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '18' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 694s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '21' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 694s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '27' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 694s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '28' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 694s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '30' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 694s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '34' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 694s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '35' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 694s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '39' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 694s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '45' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 694s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '48' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 694s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 694s Warning: skipping read '56' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 694s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '59' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 694s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '61' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 694s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '62' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 694s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '66' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 694s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '67' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 694s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 694s Warning: skipping read '74' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 694s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '78' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 694s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '83' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 694s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '84' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 694s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '85' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 694s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '93' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 694s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '95' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 694s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '100' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 694s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '101' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 694s Warning: skipping read '105' because length (1) <= # seed mismatches (0) 694s Warning: skipping read '105' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 694s Warning: skipping read '111' because length (1) <= # seed mismatches (0) 694s Warning: skipping read '111' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 694s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '121' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 694s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '122' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 694s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '124' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 694s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '127' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 694s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '129' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 694s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '131' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 694s 145 reads; of these: 694s 145 (100.00%) were unpaired; of these: 694s 125 (86.21%) aligned 0 times 694s 9 (6.21%) aligned exactly 1 time 694s 11 (7.59%) aligned >1 times 694s 13.79% overall alignment rate 694s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 694s Flattened IUPAC characters 694s Mutating sequence Sim.pm.2 694s Introducing 13 SNPs, 3/0 ref/read gaps, and 3 rearrangements 694s Finished SNPs 694s Finished ref gaps 694s Finished read gaps 694s Mutating sequence Sim.pm.1 694s Introducing 16 SNPs, 0/0 ref/read gaps, and 3 rearrangements 694s Finished SNPs 694s Finished ref gaps 694s Finished read gaps 694s Mutated reference genome to subject genome 694s SNPs introduced: 29 694s Reference gaps introduced: 3 694s Read gaps introduced: 0 694s Rearrangements introduced: 6 694s Created read sampler 694s Sampling 97 reads 694s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 694s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 694s parsing sequence Sim.pm.1... 694s parsing sequence Sim.pm.2... 694s *** Run 42 of 100 694s /usr/bin/bowtie2 --trim3 7 --nofw --rfg 23.2662414194227,11.7618205955973 --trim5 9 --local --cp-ival 3 --score-min L,5.98315488061317,1.20040291828767 -D 21 -R 1 --rdg 46.3598761789452 --large-index --np 1 --cp-min 5 -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta 694s Parsed 234 reference bases 694s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '1' because it was < 2 characters long 694s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '6' because it was < 2 characters long 694s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '13' because it was < 2 characters long 694s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '20' because it was < 2 characters long 694s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '22' because it was < 2 characters long 694s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '34' because it was < 2 characters long 694s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '37' because it was < 2 characters long 694s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '41' because it was < 2 characters long 694s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '47' because it was < 2 characters long 694s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '49' because it was < 2 characters long 694s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '51' because it was < 2 characters long 694s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '54' because it was < 2 characters long 694s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '59' because it was < 2 characters long 694s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '64' because it was < 2 characters long 694s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 694s Read 50 alignments... 694s Warning: skipping mate #1 of read '75' because it was < 2 characters long 694s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '78' because it was < 2 characters long 694s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '85' because it was < 2 characters long 694s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '86' because it was < 2 characters long 694s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '87' because it was < 2 characters long 694s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '88' because it was < 2 characters long 694s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '89' because it was < 2 characters long 694s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '90' because it was < 2 characters long 694s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '92' because it was < 2 characters long 694s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '93' because it was < 2 characters long 694s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '95' because it was < 2 characters long 694s 97 reads; of these: 694s 73 (75.26%) were paired; of these: 694s 73 (100.00%) aligned concordantly 0 times 694s 0 (0.00%) aligned concordantly exactly 1 time 694s 0 (0.00%) aligned concordantly >1 times 694s ---- 694s 73 pairs aligned concordantly 0 times; of these: 694s 0 (0.00%) aligned discordantly 1 time 694s ---- 694s 73 pairs aligned 0 times concordantly or discordantly; of these: 694s 146 mates make up the pairs; of these: 694s 139 (95.21%) aligned 0 times 694s 6 (4.11%) aligned exactly 1 time 694s 1 (0.68%) aligned >1 times 694s 24 (24.74%) were unpaired; of these: 694s 22 (91.67%) aligned 0 times 694s 2 (8.33%) aligned exactly 1 time 694s 0 (0.00%) aligned >1 times 694s 5.29% overall alignment rate 694s Read 100 alignments... 694s Read 150 alignments... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTT 694s TGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGGTTCGCCGTTCCGGGTTTGTCGTTGTAGGCCGATGGGGTTCGCCGTTCCCGGTTTGTCGTTGTAGGC 694s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GTCGTTGTAGGCCGATGGGGTTCGCCGTTCCCGGTTTGTCGTTGTAGGCCGTTGGGGTTCCCT 694s GTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCCCT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GACGCCGTTGAA 694s GACGCCGTTGAA 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GTTGGTTTATGTCATCG 694s GTTGGTTTATGTCATCG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CATCGCGCGGTTGT 694s CATCGCGCGGTTGT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CGCCGTTGAACGTGC 694s CGCCGTTGAACGTGC 694s Processing line... 694s Processing line... 694s GGCGGTGCCAGTCCGATTCGGTTGGTTTATGTGATCGCGCGGTTTTTTGGTGTGTACGGGGGTCTCAGGTTGGAG 694s GGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTCGCCGTTCCCGGTTTGTCGTT 694s TTCGCCGTTCCCGGTGTGTCGTT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s --- Summary --- 694s Read 1 reference strings 694s Checked 9 alignments, 0 edits 694s --------------- 694s PASSED 694s Flattened IUPAC characters 694s Mutating sequence Sim.pm.2 694s Introducing 10 SNPs, 1/1 ref/read gaps, and 2 rearrangements 694s Finished SNPs 694s Finished ref gaps 694s Finished read gaps 694s Mutating sequence Sim.pm.1 694s Introducing 6 SNPs, 0/0 ref/read gaps, and 2 rearrangements 694s Finished SNPs 694s Finished ref gaps 694s Finished read gaps 694s Mutated reference genome to subject genome 694s SNPs introduced: 16 694s Reference gaps introduced: 1 694s Read gaps introduced: 1 694s Rearrangements introduced: 4 694s Created read sampler 694s Sampling 210 reads 694s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 694s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 694s parsing sequence Sim.pm.1... 694s parsing sequence Sim.pm.2... 694s Parsed 234 reference bases 694s *** Run 43 of 100 694s /usr/bin/bowtie2 -M 3 --large-index --np 6 --cp-min 2 --trim5 2 --cp-ival 1 --score-min L,3.84684255532064,1.05637586572764 --ma 13.3210604052479 -R 3 -i S,2.48954289947224 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 694s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 694s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 694s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '3' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 694s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '33' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 694s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '36' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 694s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '50' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 694s Read 50 alignments... 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 694s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '73' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 694s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '80' because it was < 2 characters long 694s Read 100 alignments... 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 694s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '85' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 694s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '90' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 694s Warning: skipping mate #1 of read '92' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '92' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 694s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '95' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 694s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '100' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 694s Read 150 alignments... 694s Read 200 alignments... 694s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 694s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '119' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 694s Warning: skipping mate #1 of read '121' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '121' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 694s Warning: skipping mate #1 of read '135' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '135' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 694s Warning: skipping mate #1 of read '142' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '142' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 694s Warning: skipping mate #1 of read '145' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '145' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 694s Warning: skipping mate #1 of read '149' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '149' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 694s Warning: skipping mate #1 of read '151' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '151' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 694s Warning: skipping mate #1 of read '159' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '159' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 694s Read 250 alignments... 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 694s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '178' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 694s Read 300 alignments... 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 694s Warning: skipping mate #1 of read '189' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '189' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 694s Warning: skipping mate #1 of read '194' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '194' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 694s Warning: skipping mate #2 of read '199' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '199' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '201; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '201; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '202; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '202; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '203; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '203; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '204; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '204; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '205; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '205; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '206; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '206; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '207; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '207; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '208; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '208; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '209; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '209; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '210; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '210; setting to 0 instead 694s 210 reads; of these: 694s 201 (95.71%) were paired; of these: 694s 200 (99.50%) aligned concordantly 0 times 694s 1 (0.50%) aligned concordantly exactly 1 time 694s 0 (0.00%) aligned concordantly >1 times 694s ---- 694s 200 pairs aligned concordantly 0 times; of these: 694s 2 (1.00%) aligned discordantly 1 time 694s ---- 694s 198 pairs aligned 0 times concordantly or discordantly; of these: 694s 396 mates make up the pairs; of these: 694s 325 (82.07%) aligned 0 times 694s 28 (7.07%) aligned exactly 1 time 694s 43 (10.86%) aligned >1 times 694s 9 (4.29%) were unpaired; of these: 694s 7 (77.78%) aligned 0 times 694s 1 (11.11%) aligned exactly 1 time 694s 1 (11.11%) aligned >1 times 694s 19.22% overall alignment rate 694s Read 350 alignments... 694s Read 400 alignments... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTGGTTTAT 694s TTGGTTTAT 694s Processing line... 694s Processing line... 694s TTGTAGGCCGTTG 694s TTGTAGGCCGTTG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCC 694s GGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGC 694s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GCGTG 694s GCGTG 694s Processing line... 694s Processing line... 694s GGGG 694s GGGG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CGCCGTTCCCGGTGTGTCGTTGTAGGC 694s CGCCGTTCCCGGTGTGTCGTTGTAGGC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TCGCCGTTCCCGGT 694s TCGCCGTTCCCGGT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TA 694s TA 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGTT 694s GGTT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CCGTTG 694s CCGTTG 694s Processing line... 694s Processing line... 694s GTGTGTCGTTGTAGGCCGTTGGGGTTCC 694s GTGTGTCGTTGTAGGCCGTTGGGGTTCC 694s Processing line... 694s Processing line... 694s GTTCCCGG 694s GTTCCCGG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGTG 694s GGTG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTCCCGGTGTGTCGT 694s TTCCCGGTGTGTCGT 694s Processing line... 694s Processing line... 694s TGTC 694s TGTC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTCCCGGTGTGTC 694s TTCCCGGTGTGTC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GA 694s GA 694s Processing line... 694s Processing line... 694s GGTCTC 694s GGTCTC 694s Processing line... 694s Processing line... 694s CCGT 694s CCGT 694s Processing line... 694s TCAGGTTG 694s TCAGGTTG 694s Processing line... 694s CGGGGCCA 694s CGGGGCCA 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s ATT 694s ATT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TCG 694s TCG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTC 694s TTC 694s Processing line... 694s Processing line... 694s GTCTCAGGTT 694s GTCTCAGGTT 694s Processing line... 694s Processing line... 694s GCGTGGGTGCGGCGGG 694s GCGTGGGTGCGGCGGG 694s Processing line... 694s Processing line... 694s TGGTGACGCCGTTGAACGTGCGG 694s TGGTGACGCCGTTGAACGTGCGG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TCGCGCG 694s TCGCGCG 694s Processing line... 694s CGGGGGTCTCAGGTTGGAGTCC 694s CGGGGGTCTCAGGTTGGAGTCC 694s Processing line... 694s Processing line... 694s Processing line... 694s TAGGCCGTTG 694s TAGGCCGTTG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGGCGTGGGTGCGGCGGGGCCAG 694s GGGCGTGGGTGCGGCGGGGCCAG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGGG 694s GGGG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TGTCAT 694s TGTCAT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGTTCG 694s GGTTCG 694s Processing line... 694s Processing line... 694s GGTGT 694s GGTGT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GTA 694s GTA 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CGCCG 694s CGCCG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GCCA 694s GCCA 694s Processing line... 694s Processing line... 694s TTGTA 694s TTGTA 694s Processing line... 694s Processing line... 694s GCCCG 694s GCCCG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TG 694s TG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s AGTC 694s AGTC 694s Processing line... 694s Processing line... 694s TGTGTCGTTGTAGGCC 694s TGTGTCGTTGTAGGCC 694s Processing line... 694s Processing line... 694s GCCGTTGAACGTGCGGCGG 694s GCCGTTGAACGTGCGGCGG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TTGGAGTCCCGCGGCCCG 694s TTGGAGTCCCGCGGCCCG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CGTTGGGGTTCC 694s CGTTGGGGTTCC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GTAGGC 694s GTAGGC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GTTGAACGTGCGG 694s GTTGAACGTGCGG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGCGTGGGTGCGGCGGGGCC 694s GGCGTGGGTGCGGCGGGGCC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TCAGGTTGGAG 694s TCAGGTTGGAG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GTCG 694s GTCG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGGTT 694s GGGTT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TCGTTGT 694s TCGTTGT 694s Processing line... 694s Processing line... 694s CCGTTGAACGTGCGGCGGGGCCA 694s CCGTTGAACGTGCGGCGGGGCCA 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CGTT 694s CGTT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GG 694s GG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TCGATTCGGT 694s TCGATTCGGT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GACG 694s GACG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TCCCGGT 694s TCCCGGT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GTTGAAC 694s GTTGAAC 694s Processing line... 694s Processing line... 694s TAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGT 694s TAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGT 694s Processing line... 694s Processing line... 694s TGGGTG 694s TGGGTG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CCCGGTG 694s CCCGGTG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s /usr/bin/bowtie2 -M 3 --large-index --np 6 --cp-min 2 --trim5 2 --cp-ival 1 --score-min L,3.84684255532064,1.05637586572764 --ma 13.3210604052479 -R 3 -i S,2.48954289947224 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 694s CCCG 694s CCCG 694s Processing line... 694s CCGTTGGGGTTCGCCGTTCCCGGTG 694s CCGTTGGGGTTCGCCGTTCCCGGTG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TCGTTGTAG 694s TCGTTGTAG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GTT 694s GTT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GGTGCG 694s GGTGCG 694s Processing line... 694s CCGTTGGGGTTCCCT 694s CCGTTGGGGTTCCCT 694s Processing line... 694s TCCCGGTGTGTCGTTGTAG 694s TCCCGGTGTGTCGTTGTAG 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TGGGGT 694s TGGGGT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CGGTGTGTC 694s CGGTGTGTC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s GATTCGGTTGGTTTATGTC 694s GATTCGGTTGGTTTATGTC 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s CAGTTCGATTCG 694s CAGTTCGATTCG 694s Processing line... 694s Processing line... 694s GGTTGGA 694s GGTTGGA 694s Processing line... 694s GCGGTTGT 694s GCGGTTGT 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s Processing line... 694s TGCGGCGGGGCCA 694s TGCGGCGGGGCCA 694s Processing line... 694s Processing line... 694s CGTTGG 694s CGTTGG 694s Processing line... 694s --- Summary --- 694s Read 1 reference strings 694s Checked 79 alignments, 0 edits 694s --------------- 694s PASSED 694s ALSO checking that bowtie2 and bowtie2-align match up 694s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 694s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 694s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '3' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 694s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '33' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 694s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '36' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 694s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 694s Warning: skipping read '50' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 694s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '73' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 694s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #2 of read '80' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 694s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '85' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 694s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '90' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 694s Warning: skipping mate #1 of read '92' because length (1) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '92' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 694s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '95' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 694s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 694s Warning: skipping mate #1 of read '100' because it was < 2 characters long 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 694s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 695s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '119' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 695s Warning: skipping mate #1 of read '121' because length (1) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '121' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 695s Warning: skipping mate #1 of read '135' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '135' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 695s Warning: skipping mate #1 of read '142' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '142' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 695s Warning: skipping mate #1 of read '145' because length (1) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '145' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 695s Warning: skipping mate #1 of read '149' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '149' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 695s Warning: skipping mate #1 of read '151' because length (1) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '151' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 695s Warning: skipping mate #1 of read '159' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '159' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 695s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '178' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 695s Warning: skipping mate #1 of read '189' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '189' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 695s Warning: skipping mate #1 of read '194' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '194' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 695s Warning: skipping mate #2 of read '199' because length (1) <= # seed mismatches (0) 695s Warning: skipping mate #2 of read '199' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '201; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '201; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '202; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '202; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '203; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '203; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '204; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '204; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '205; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '205; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '206; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '206; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '207; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '207; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '208; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '208; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '209; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '209; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '210; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '210; setting to 0 instead 695s 210 reads; of these: 695s 201 (95.71%) were paired; of these: 695s 200 (99.50%) aligned concordantly 0 times 695s 1 (0.50%) aligned concordantly exactly 1 time 695s 0 (0.00%) aligned concordantly >1 times 695s ---- 695s 200 pairs aligned concordantly 0 times; of these: 695s 2 (1.00%) aligned discordantly 1 time 695s ---- 695s 198 pairs aligned 0 times concordantly or discordantly; of these: 695s 396 mates make up the pairs; of these: 695s 325 (82.07%) aligned 0 times 695s 28 (7.07%) aligned exactly 1 time 695s 43 (10.86%) aligned >1 times 695s 9 (4.29%) were unpaired; of these: 695s 7 (77.78%) aligned 0 times 695s 1 (11.11%) aligned exactly 1 time 695s 1 (11.11%) aligned >1 times 695s 19.22% overall alignment rate 695s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 695s /usr/bin/bowtie2 -M 3 --large-index --np 6 --cp-min 2 --trim5 2 --cp-ival 1 --score-min L,3.84684255532064,1.05637586572764 --ma 13.3210604052479 -R 3 -i S,2.48954289947224 -q -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 695s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 695s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 695s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 695s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '3' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 695s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '33' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 695s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '36' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 695s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 695s Warning: skipping read '50' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 695s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '73' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 695s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 695s Warning: skipping mate #2 of read '80' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 695s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '85' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 695s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '90' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 695s Warning: skipping mate #1 of read '92' because length (1) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '92' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 695s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '95' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 695s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '100' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 695s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '119' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 695s Warning: skipping mate #1 of read '121' because length (1) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '121' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 695s Warning: skipping mate #1 of read '135' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '135' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 695s Warning: skipping mate #1 of read '142' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '142' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 695s Warning: skipping mate #1 of read '145' because length (1) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '145' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 695s Warning: skipping mate #1 of read '149' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '149' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 695s Warning: skipping mate #1 of read '151' because length (1) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '151' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 695s Warning: skipping mate #1 of read '159' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '159' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 695s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '178' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 695s Warning: skipping mate #1 of read '189' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '189' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 695s Warning: skipping mate #1 of read '194' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '194' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 695s Warning: skipping mate #2 of read '199' because length (1) <= # seed mismatches (0) 695s Warning: skipping mate #2 of read '199' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '201; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '201; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '202; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '202; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '203; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '203; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '204; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '204; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '205; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '205; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '206; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '206; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '207; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '207; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '208; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '208; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '209; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '209; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '210; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '210; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 695s 210 reads; of these: 695s 201 (95.71%) were paired; of these: 695s 200 (99.50%) aligned concordantly 0 times 695s 1 (0.50%) aligned concordantly exactly 1 time 695s 0 (0.00%) aligned concordantly >1 times 695s ---- 695s 200 pairs aligned concordantly 0 times; of these: 695s 2 (1.00%) aligned discordantly 1 time 695s ---- 695s 198 pairs aligned 0 times concordantly or discordantly; of these: 695s 396 mates make up the pairs; of these: 695s 325 (82.07%) aligned 0 times 695s 28 (7.07%) aligned exactly 1 time 695s 43 (10.86%) aligned >1 times 695s 9 (4.29%) were unpaired; of these: 695s 7 (77.78%) aligned 0 times 695s 1 (11.11%) aligned exactly 1 time 695s 1 (11.11%) aligned >1 times 695s 19.22% overall alignment rate 695s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 695s Flattened IUPAC characters 695s Mutating sequence Sim.pm.1 695s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 695s Finished SNPs 695s Finished ref gaps 695s Finished read gaps 695s Mutating sequence Sim.pm.2 695s Introducing 18 SNPs, 1/2 ref/read gaps, and 1 rearrangements 695s Finished SNPs 695s Finished ref gaps 695s Finished read gaps 695s Mutated reference genome to subject genome 695s SNPs introduced: 24 695s Reference gaps introduced: 2 695s Read gaps introduced: 2 695s Rearrangements introduced: 1 695s Created read sampler 695s Sampling 37 reads 695s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 695s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 695s parsing sequence Sim.pm.1... 695s parsing sequence Sim.pm.2... 695s *** Run 44 of 100 695s /usr/bin/bowtie2 --rfg 26.082962778421,8.2456562751349 -i C,0.641987416692511 --gbar 5 --score-min L,3.58992018510737,9.37687309134482 --cp-ival 2 --local --trim5 1 --cp-min 5 --large-index -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta 695s Parsed 234 reference bases 695s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '14' because it was < 2 characters long 695s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '25' because it was < 2 characters long 695s 37 reads; of these: 695s 37 (100.00%) were paired; of these: 695s 37 (100.00%) aligned concordantly 0 times 695s 0 (0.00%) aligned concordantly exactly 1 time 695s 0 (0.00%) aligned concordantly >1 times 695s ---- 695s 37 pairs aligned concordantly 0 times; of these: 695s 0 (0.00%) aligned discordantly 1 time 695s ---- 695s 37 pairs aligned 0 times concordantly or discordantly; of these: 695s 74 mates make up the pairs; of these: 695s 74 (100.00%) aligned 0 times 695s 0 (0.00%) aligned exactly 1 time 695s 0 (0.00%) aligned >1 times 695s 0.00% overall alignment rate 695s Read 50 alignments... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s --- Summary --- 695s Read 1 reference strings 695s Checked 0 alignments, 0 edits 695s --------------- 695s PASSED 695s ALSO checking that bowtie2 and bowtie2-align match up 695s /usr/bin/bowtie2 --rfg 26.082962778421,8.2456562751349 -i C,0.641987416692511 --gbar 5 --score-min L,3.58992018510737,9.37687309134482 --cp-ival 2 --local --trim5 1 --cp-min 5 --large-index -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 695s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '14' because it was < 2 characters long 695s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '25' because it was < 2 characters long 695s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 695s 37 reads; of these: 695s 37 (100.00%) were paired; of these: 695s 37 (100.00%) aligned concordantly 0 times 695s 0 (0.00%) aligned concordantly exactly 1 time 695s 0 (0.00%) aligned concordantly >1 times 695s ---- 695s 37 pairs aligned concordantly 0 times; of these: 695s 0 (0.00%) aligned discordantly 1 time 695s ---- 695s 37 pairs aligned 0 times concordantly or discordantly; of these: 695s 74 mates make up the pairs; of these: 695s 74 (100.00%) aligned 0 times 695s 0 (0.00%) aligned exactly 1 time 695s 0 (0.00%) aligned >1 times 695s 0.00% overall alignment rate 695s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 695s /usr/bin/bowtie2 --rfg 26.082962778421,8.2456562751349 -i C,0.641987416692511 --gbar 5 --score-min L,3.58992018510737,9.37687309134482 --cp-ival 2 --local --trim5 1 --cp-min 5 --large-index -f -p 3 -x /tmp/Sim.pm.RKKEKvBt --reorder -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 695s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '14' because it was < 2 characters long 695s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '25' because it was < 2 characters long 695s 37 reads; of these: 695s 37 (100.00%) were paired; of these: 695s 37 (100.00%) aligned concordantly 0 times 695s 0 (0.00%) aligned concordantly exactly 1 time 695s 0 (0.00%) aligned concordantly >1 times 695s ---- 695s 37 pairs aligned concordantly 0 times; of these: 695s 0 (0.00%) aligned discordantly 1 time 695s ---- 695s 37 pairs aligned 0 times concordantly or discordantly; of these: 695s 74 mates make up the pairs; of these: 695s 74 (100.00%) aligned 0 times 695s 0 (0.00%) aligned exactly 1 time 695s 0 (0.00%) aligned >1 times 695s 0.00% overall alignment rate 695s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 695s Flattened IUPAC characters 695s Mutating sequence Sim.pm.2 695s Introducing 1 SNPs, 2/0 ref/read gaps, and 0 rearrangements 695s Finished SNPs 695s Finished ref gaps 695s Finished read gaps 695s Mutating sequence Sim.pm.1 695s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 695s Finished SNPs 695s Finished ref gaps 695s Finished read gaps 695s *** Run 45 of 100 695s /usr/bin/bowtie2 --score-min L,6.12820883788995,6.0578666631685 --gbar 8 --large-index --cp-min 7 --trim5 7 --cp-ival 1 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 695s Mutated reference genome to subject genome 695s SNPs introduced: 5 695s Reference gaps introduced: 2 695s Read gaps introduced: 1 695s Rearrangements introduced: 0 695s Created read sampler 695s Sampling 103 reads 695s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 695s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 695s parsing sequence Sim.pm.1... 695s parsing sequence Sim.pm.2... 695s Parsed 234 reference bases 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 695s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '1' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 695s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '12' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 695s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '15' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 695s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '23' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 695s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '28' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 695s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '32' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 695s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '37' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 695s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 695s Warning: skipping read '51' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 695s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '60' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 695s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '61' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 695s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '62' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 695s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '64' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 695s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 695s Warning: skipping read '66' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 695s Warning: skipping mate #1 of read '68' because length (1) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '68' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 695s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '72' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 695s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '77' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 695s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '78' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 695s Read 50 alignments... 695s Read 100 alignments... 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 695s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '91' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 695s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '95' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 695s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '97' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 695s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 695s Warning: skipping mate #1 of read '99' because it was < 2 characters long 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 695s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 695s 103 reads; of these: 695s 87 (84.47%) were paired; of these: 695s 83 (95.40%) aligned concordantly 0 times 695s 2 (2.30%) aligned concordantly exactly 1 time 695s 2 (2.30%) aligned concordantly >1 times 695s ---- 695s 83 pairs aligned concordantly 0 times; of these: 695s 2 (2.41%) aligned discordantly 1 time 695s ---- 695s 81 pairs aligned 0 times concordantly or discordantly; of these: 695s 162 mates make up the pairs; of these: 695s 136 (83.95%) aligned 0 times 695s 12 (7.41%) aligned exactly 1 time 695s 14 (8.64%) aligned >1 times 695s 16 (15.53%) were unpaired; of these: 695s 13 (81.25%) aligned 0 times 695s 1 (6.25%) aligned exactly 1 time 695s 2 (12.50%) aligned >1 times 695s 21.58% overall alignment rate 695s Read 150 alignments... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s AGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGT 695s AGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGT 695s Processing line... 695s GCGGCGGGGCCAGTTCGATTCGG 695s GCGGCGGGGCCAGTTCGATTCGG 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s GCGTGGGT 695s GCGTGGGT 695s Processing line... 695s ACGCCGTTGAACGTG 695s ACGCCGTTGAACGTG 695s Processing line... 695s CGCCGTTCCC 695s CGCCGTTCCC 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s CATCGCGCGGTTGTTTGGTG 695s CATCGCGCGGTTGTTTGGTG 695s Processing line... 695s Processing line... 695s CGCCGTTCCCGGTGTGTCG 695s CGCCGTTCCCGGTGTGTCG 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s CGTGGG 695s CGTGGG 695s Processing line... 695s TCATCGCGCGGTTG 695s TCATCGCGCGGTTG 695s Processing line... 695s Processing line... 695s Processing line... 695s TTCGGTTGGTTTATGTCATCGCGCGGTTGTTT 695s TTCGGTTGGTTTATGTCATCGCGCGGTTGTTT 695s Processing line... 695s TTCGGTTGGTTTATGTCA 695s TTCGGTTGGTTTATGTCA 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s TGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCC 695s TGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCC 695s Processing line... 695s Processing line... 695s CC 695s CC 695s Processing line... 695s Processing line... 695s CCGTTGA 695s CCGTTGA 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s CGCCG 695s CGCCG 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s CGGTGTGTCGTTGTAGGCCGTT 695s CGGTGTGTCGTTGTAGGCCGTT 695s Processing line... 695s Processing line... 695s CGCCGTTCCCGGTGTGTCGTTGTAG 695s CGCCGTTCCCGGTGTGTCGTTGTAG 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s TCGCC 695s TCGCC 695s Processing line... 695s CCCGGTGTGTCGTTGTAGGCCGTTGGGGT 695s CCCGGTGTGTCGTTGTAGGCCGTTGGGGT 695s Processing line... 695s CCGTTGGGGTTCG 695s CCGTTGGGGTTCG 695s Processing line... 695s Processing line... 695s GGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCAT 695s GGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCAT 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s CGGTTGGTTTATGTC 695s CGGTTGGTTTATGTC 695s Processing line... 695s Processing line... 695s CCAGTTCGATTCGGTTGGTTTATGTCAT 695s CCAGTTCGATTCGGTTGGTTTATGTCAT 695s Processing line... 695s CGGCGGGGCCAGTTCGATTCGG 695s CGGCGGGGCCAGTTCGATTCGG 695s Processing line... 695s TTCCCGGTGTGT 695s TTCCCGGTGTGT 695s Processing line... 695s TT 695s TT 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s GTTCG 695s GTTCG 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s TTGAA 695s TTGAA 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s CCCG 695s CCCG 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s GGGTTCGCCGTTCCCGGTG 695s GGGTTCGCCGTTCCCGGTG 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s GGGC 695s GGGC 695s Processing line... 695s Processing line... 695s Processing line... 695s CGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 695s CGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s CCCGG 695s CCCGG 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s TGTGTCGTTGTAGGCCGTTGGGG 695s TGTGTCGTTGTAGGCCGTTGGGG 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s TG 695s TG 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s GGCCGT 695s GGCCGT 695s Processing line... 695s Processing line... 695s TGTCGTTGTAGGCCGTTGGGGTTCG 695s TGTCGTTGTAGGCCGTTGGGGTTCG 695s Processing line... 695s Processing line... 695s GTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGT 695s GTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGT 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s CCGTT 695s CCGTT 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s TTGTAGG 695s TTGTAGG 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s TGTCATCGCGCGGTTGTTTGGTGTGT 695s TGTCATCGCGCGGTTGTTTGGTGTGT 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s --- Summary --- 695s Read 1 reference strings 695s Checked 41 alignments, 0 edits 695s --------------- 695s PASSED 695s Flattened IUPAC characters 695s Mutating sequence Sim.pm.1 695s Introducing 0 SNPs, 2/1 ref/read gaps, and 0 rearrangements 695s Finished SNPs 695s Finished ref gaps 695s Finished read gaps 695s Mutating sequence Sim.pm.2 695s Introducing 1 SNPs, 1/0 ref/read gaps, and 1 rearrangements 695s Finished SNPs 695s Finished ref gaps 695s Finished read gaps 695s Mutated reference genome to subject genome 695s SNPs introduced: 1 695s Reference gaps introduced: 3 695s Read gaps introduced: 1 695s Rearrangements introduced: 1 695s Created read sampler 695s Sampling 130 reads 695s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 695s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 695s parsing sequence Sim.pm.1... 695s parsing sequence Sim.pm.2... 695s Parsed 234 reference bases 695s *** Run 46 of 100 695s /usr/bin/bowtie2 --gbar 3 --score-min L,2.59847046754788,6.40209182639504 --rdg 1.98998749123371,14.091488067888 --large-index --cp-min 10 -i C,0.654744680809462,7.82783886295106 --trim3 1 --rfg 34.9174551535322 --n-ceil 0.636130498755301,1.12205763318338 -M 7 --cp-ival 2 --local -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 695s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 695s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 695s Warning: skipping read '34' because it was < 2 characters long 695s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 695s Warning: skipping read '39' because it was < 2 characters long 695s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 695s Warning: skipping read '49' because it was < 2 characters long 695s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 695s Warning: skipping read '58' because it was < 2 characters long 695s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 695s Warning: skipping read '75' because it was < 2 characters long 695s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 695s Warning: skipping read '79' because it was < 2 characters long 695s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 695s Warning: skipping read '91' because it was < 2 characters long 695s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 695s Warning: skipping read '94' because it was < 2 characters long 695s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 695s Warning: skipping read '96' because it was < 2 characters long 695s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 695s Warning: skipping read '102' because it was < 2 characters long 695s Warning: skipping read '112' because length (1) <= # seed mismatches (0) 695s Warning: skipping read '112' because it was < 2 characters long 695s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 695s Warning: skipping read '127' because it was < 2 characters long 695s Read 50 alignments... 695s Read 100 alignments... 695s 130 reads; of these: 695s 130 (100.00%) were unpaired; of these: 695s 130 (100.00%) aligned 0 times 695s 0 (0.00%) aligned exactly 1 time 695s 0 (0.00/usr/bin/bowtie2 --gbar 3 --score-min L,2.59847046754788,6.40209182639504 --rdg 1.98998749123371,14.091488067888 --large-index --cp-min 10 -i C,0.654744680809462,7.82783886295106 --trim3 1 --rfg 34.9174551535322 --n-ceil 0.636130498755301,1.12205763318338 -M 7 --cp-ival 2 --local -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 695s %) aligned >1 times 695s 0.00% overall alignment rate 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s Processing line... 695s --- Summary --- 695s Read 1 reference strings 695s Checked 0 alignments, 0 edits 695s --------------- 695s PASSED 695s ALSO checking that bowtie2 and bowtie2-align match up 696s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 696s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '34' because it was < 2 characters long 696s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '39' because it was < 2 characters long 696s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '49' because it was < 2 characters long 696s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '58' because it was < 2 characters long 696s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '75' because it was < 2 characters long 696s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '79' because it was < 2 characters long 696s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '91' because it was < 2 characters long 696s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '94' because it was < 2 characters long 696s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '96' because it was < 2 characters long 696s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '102' because it was < 2 characters long 696s Warning: skipping read '112' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '112' because it was < 2 characters long 696s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '127' because it was < 2 characters long 696s 130 reads; of these: 696s 130 (100.00%) were unpaired; of these: 696s 130 (100.00%) aligned 0 times 696s 0 (0.00%) aligned exactly 1 time 696s 0 (0.00%) aligned >1 times 696s 0.00% overall alignment rate 696s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 696s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 696s /usr/bin/bowtie2 --gbar 3 --score-min L,2.59847046754788,6.40209182639504 --rdg 1.98998749123371,14.091488067888 --large-index --cp-min 10 -i C,0.654744680809462,7.82783886295106 --trim3 1 --rfg 34.9174551535322 --n-ceil 0.636130498755301,1.12205763318338 -M 7 --cp-ival 2 --local -q -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 696s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 696s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '34' because it was < 2 characters long 696s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '39' because it was < 2 characters long 696s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '49' because it was < 2 characters long 696s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '58' because it was < 2 characters long 696s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '75' because it was < 2 characters long 696s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '79' because it was < 2 characters long 696s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '91' because it was < 2 characters long 696s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '94' because it was < 2 characters long 696s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '96' because it was < 2 characters long 696s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '102' because it was < 2 characters long 696s Warning: skipping read '112' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '112' because it was < 2 characters long 696s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 696s Warning: skipping read '127' because it was < 2 characters long 696s 130 reads; of these: 696s 130 (100.00%) were unpaired; of these: 696s 130 (100.00%) aligned 0 times 696s 0 (0.00%) aligned exactly 1 time 696s 0 (0.00%) aligned >1 times 696s 0.00% overall alignment rate 696s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 696s Flattened IUPAC characters 696s Mutating sequence Sim.pm.1 696s Introducing 13 SNPs, 0/3 ref/read gaps, and 0 rearrangements 696s Finished SNPs 696s Finished ref gaps 696s Finished read gaps 696s Mutating sequence Sim.pm.2 696s Introducing 5 SNPs, 2/0 ref/read gaps, and 0 rearrangements 696s Finished SNPs 696s Finished ref gaps 696s Finished read gaps 696s Mutated reference genome to subject genome 696s SNPs introduced: 18 696s Reference gaps introduced: 2 696s Read gaps introduced: 3 696s Rearrangements introduced: 0 696s Created read sampler 696s Sampling 203 reads 696s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 696s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 696s parsing sequence Sim.pm.1... 696s parsing sequence Sim.pm.2... 696s *** Run 47 of 100 696s /usr/bin/bowtie2 -N 0 -L17 --cp-ival 2 --local --n-ceil 1.25881718983849,0.466470879106794 -a --mm --score-min L,6.93839657714763,2.52857371136954 --large-index --cp-min 4 --np 2 -f -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta 696s Parsed 234 reference bases 696s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '54' because it was < 2 characters long 696s Read 50 alignments... 696s Warning: skipping read '162' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '162' because it was < 2 characters long 696s Warning: skipping read '175' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '175' because it was < 2 characters long 696s Warning: skipping read '185' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '185' because it was < 2 characters long 696s Warning: skipping read '195' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '195' because it was < 2 characters long 696s Warning: skipping read '198' because length (1) <= # seed mismatches (0) 696s Warning: skipping read '198' because it was < 2 characters long 696s Read 100 alignments... 696s 203 reads; of these: 696s 203 (100.00%) were unpaired; of these: 696s 203 (100.00%) aligned 0 times 696s 0 (0.00%) aligned exactly 1 time 696s 0 (0.00%) aligned >1 times 696s 0.00% overall alignment rate 696s Read 150 alignments... 696s Read 200 alignments... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s --- Summary --- 696s Read 1 reference strings 696s Checked 0 alignments, 0 edits 696s --------------- 696s PASSED 696s Flattened IUPAC characters 696s Mutating sequence Sim.pm.1 696s Introducing 9 SNPs, 2/0 ref/read gaps, and 1 rearrangements 696s Finished SNPs 696s Finished ref gaps 696s Finished read gaps 696s Mutating sequence Sim.pm.2 696s Introducing 2 SNPs, 4/2 ref/read gaps, and 0 rearrangements 696s Finished SNPs 696s Finished ref gaps 696s Finished read gaps 696s Mutated reference genome to subject genome 696s SNPs introduced: 11 696s Reference gaps introduced: 6 696s Read gaps introduced: 2 696s Rearrangements introduced: 1 696s Created read sampler 696s Sampling 63 reads 696s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 696s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 696s parsing sequence Sim.pm.1... 696s parsing sequence Sim.pm.2... 696s Parsed 234 reference bases 696s *** Run 48 of 100 696s /usr/bin/bowtie2 -k 3 -D 5 --gbar 8 --score-min L,8.19975272797932,2.10256765257486 --mm --np 1 --cp-min 2 --large-index -i S,0.466855596603232 --mp 4.70960482876581,4.66171984385987 --trim3 7 --nofw --rfg 13.2452008667598,16.4365052953842 --cp-ival 1 --local -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 696s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 696s Warning: skipping mate #1 of read '3' because it was < 2 characters long 696s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 696s Warning: skipping mate #1 of read '10' because it was < 2 characters long 696s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 696s Warning: skipping mate #2 of read '11' because it was < 2 characters long 696s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 696s Warning: skipping mate #1 of read '13' because it was < 2 characters long 696s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 696s Warning: skipping mate #1 of read '21' because it was < 2 characters long 696s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 696s Warning: skipping mate #1 of read '26' because it was < 2 characters long 696s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 696s Warning: skipping mate #1 of read '27' because it was < 2 characters long 696s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 696s Warning: skipping mate #2 of read '45' because it was < 2 characters long 696s 63 reads; of these: 696s 59 (93.65%) were paired; of these: 696s 59 (100.00%) aligned concordantly 0 times 696s 0 (0.00%) aligned concordantly exactly 1 time 696s 0 (0.00%) aligned concordantly >1 times 696s ---- 696s 59 pairs aligned concordantly 0 times; of these: 696s 0 (0.00%) aligned discordantly 1 time 696s ---- 696s 59 pairs aligned 0 times concordantly or discordantly; of these: 696s 118 mates make up the pairs; of these: 696s 118 (100.00%) aligned 0 times 696s 0 (0.00%) aligned exactly 1 time 696s 0 (0.00%) aligned >1 times 696s 4 (6.35%) were unpaired; of these: 696s 4 (100.00%) aligned 0 times 696s 0 (0.00%) aligned exactly 1 time 696s 0 (0.00%) aligned >1 times 696s 0.00% overall alignment rate 696s Read 50 alignments... 696s Read 100 alignments... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s --- Summary --- 696s Read 1 reference strings 696s Checked 0 alignments, 0 edits 696s --------------- 696s PASSED 696s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 696s /usr/bin/bowtie2 -k 3 -D 5 --gbar 8 --score-min L,8.19975272797932,2.10256765257486 --mm --np 1 --cp-min 2 --large-index -i S,0.466855596603232 --mp 4.70960482876581,4.66171984385987 --trim3 7 --nofw --rfg 13.2452008667598,16.4365052953842 --cp-ival 1 --local -q -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 696s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 696s Warning: skipping mate #1 of read '3' because it was < 2 characters long 696s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 696s Warning: skipping mate #1 of read '10' because it was < 2 characters long 696s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 696s Warning: skipping mate #2 of read '11' because it was < 2 characters long 696s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 696s Warning: skipping mate #1 of read '13' because it was < 2 characters long 696s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 696s Warning: skipping mate #1 of read '21' because it was < 2 characters long 696s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 696s Warning: skipping mate #1 of read '26' because it was < 2 characters long 696s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 696s Warning: skipping mate #1 of read '27' because it was < 2 characters long 696s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 696s Warning: skipping mate #2 of read '45' because it was < 2 characters long 696s 63 reads; of these: 696s 59 (93.65%) were paired; of these: 696s 59 (100.00%) aligned concordantly 0 times 696s 0 (0.00%) aligned concordantly exactly 1 time 696s 0 (0.00%) aligned concordantly >1 times 696s ---- 696s 59 pairs aligned concordantly 0 times; of these: 696s 0 (0.00%) aligned discordantly 1 time 696s ---- 696s 59 pairs aligned 0 times concordantly or discordantly; of these: 696s 118 mates make up the pairs; of these: 696s 118 (100.00%) aligned 0 times 696s 0 (0.00%) aligned exactly 1 time 696s 0 (0.00%) aligned >1 times 696s 4 (6.35%) were unpaired; of these: 696s 4 (100.00%) aligned 0 times 696s 0 (0.00%) aligned exactly 1 time 696s 0 (0.00%) aligned >1 times 696s 0.00% overall alignment rate 696s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 696s Flattened IUPAC characters 696s Mutating sequence Sim.pm.1 696s Introducing 24 SNPs, 0/0 ref/read gaps, and 0 rearrangements 696s Finished SNPs 696s Finished ref gaps 696s Finished read gaps 696s Mutating sequence Sim.pm.2 696s Introducing 14 SNPs, 1/0 ref/read gaps, and 0 rearrangements 696s Finished SNPs 696s Finished ref gaps 696s Finished read gaps 696s Mutated reference genome to subject genome 696s SNPs introduced: 38 696s Reference gaps introduced: 1 696s Read gaps introduced: 0 696s Rearrangements introduced: 0 696s Created read sampler 696s Sampling 81 reads 696s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 696s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 696s parsing sequence Sim.pm.1... 696s parsing sequence Sim.pm.2... 696s Parsed 234 reference bases 696s *** Run 49 of 100 696s /usr/bin/bowtie2 --rfg 1.54211098890725,19.1597719679496 --trim3 2 -N 1 -L18 --mp 5.74393016623057,2.69479621623535 --local --cp-ival 1 -M 6 --n-ceil 0.792033834766073,1.12526091660707 --rdg 33.4339269175584 --mm --score-min L,8.12845352427967,5.39851863676407 -R 1 -D 28 --gbar 2 --np 5 --cp-min 3 --large-index -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 696s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 696s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 696s Warning: skipping read '7' because it was < 2 characters long 696s Warning: skipping read '12' because length (1) <= # seed mismatches (1) 696s Warning: skipping read '12' because it was < 2 characters long 696s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 696s Warning: skipping read '29' because it was < 2 characters long 696s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 696s Warning: skipping read '31' because it was < 2 characters long 696s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 696s Warning: skipping read '39' because it was < 2 characters long 696s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 696s Warning: skipping read '51' because it was < 2 characters long 696s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 696s Warning: skipping read '52' because it was < 2 characters long 696s Warning: skipping read '57' because length (1) <= # seed mismatches (1) 696s Warning: skipping read '57' because it was < 2 characters long 696s 81 reads; of these: 696s 81 (100.00%) were unpaired; of these: 696s 81 (100.00%) aligned 0 times 696s 0 (0.00%) aligned exactly 1 time 696s 0 (0.00%) aligned >1 times 696s 0.00% overall alignment rate 696s Read 50 alignments... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s --- Summary --- 696s Read 1 reference strings 696s Checked 0 alignments, 0 edits 696s --------------- 696s PASSED 696s Flattened IUPAC characters 696s Mutating sequence Sim.pm.2 696s Introducing 19 SNPs, 2/3 ref/read gaps, and 1 rearrangements 696s Finished SNPs 696s Finished ref gaps 696s Finished read gaps 696s Mutating sequence Sim.pm.1 696s Introducing 11 SNPs, 0/0 ref/read gaps, and 2 rearrangements 696s Finished SNPs 696s Finished ref gaps 696s Finished read gaps 696s Mutated reference genome to subject genome 696s SNPs introduced: 30 696s Reference gaps introduced: 2 696s Read gaps introduced: 3 696s Rearrangements introduced: 3 696s Created read sampler 696s Sampling 179 reads 696s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 696s *** Run 50 of 100 696s /usr/bin/bowtie2 --n-ceil 0.096150684250895,0.0259442474717559 --large-index --cp-min 5 --cp-ival 3 --local -R 2 -i L,0.201754670892445 -N 0 --score-min L,8.33504230830753,1.30976214554616 --trim3 0 --rfg 39.4635097735554 --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq 696s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 696s parsing sequence Sim.pm.1... 696s parsing sequence Sim.pm.2... 696s Parsed 234 reference bases 696s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 696s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 696s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (1) <= # seed mismatches (0) 696s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 696s Read 50 alignments... 696s Warning: skipping read 'R_1_1_1_172_172_1/1' because length (1) <= # seed mismatches (0) 696s Read 100 alignments... 696s Warning: skipping read 'R_1_1_1_172_172_1/1' because it was < 2 characters long 696s 179 reads; of these: 696s 179 (100.00%) were unpaired; of these: 696s 158 (88.27%) aligned 0 times 696s 15 (8.38%) aligned exactly 1 time 696s 6 (3.35%) aligned >1 times 696s 11.73% overall alignment rate 696s Read 150 alignments... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s CCGTTGGGGTTCC 696s CCGTTGGGGTTCC 696s Processing line... 696s GGGCCAGTTCGATTCGGTTGGTTTATG 696s GGGCCAGTTCGATTCGGTTGGTTTATG 696s Processing line... 696s Processing line... 696s GGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGT 696s GGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGT 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s CCGTTGGGGTTCG 696s CCGTTGGGGTTCG 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s GGGTTCGCCGTTCCCGGTGTGACGTTGTAGGCAGTTGGGGTTCGCCGTTCCCGGAGTGTCGTTGGAG 696s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAG 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s CCGGTGTGTCGTTGTAGG 696s CCGGTGTGTCGTTGTAGG 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s TTCGATTCGGTTGGTTTATGTCATCGAGCGGTTG 696s TTCGATTCGGTTGGTTTATGTCATCGCGCGGTTG 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s TCGATTCGGTTGGTTTATGTCATCGAGCGGTTGTTTGGTGTGTTCGGGGGTCTCTGGTTGGAATCCCGCGGCCCGT 696s TCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGT 696s Processing line... 696s Processing line... 696s GATTCGGTTGGTTTATGTCATC 696s GATTCGGTTGGTTTATGTCATC 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s GTTCGCCGTTCCC 696s GTTCGCCGTTCCC 696s Processing line... 696s Processing line... 696s CGTTGGGGTTCGCCGTTCCC 696s CGTTGGGGTTCGCCGTTCCC 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s GACGCCGTTGAACGTG 696s GACGCCGTTGAACGTG 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s GCCAGTTCGATTCGGTTGGTTTATGTCATCGAGCGGTTGTTT 696s GCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTT 696s Processing line... 696s Processing line... 696s TTCGATTCGGTTGGTTTATGTCATCGAG 696s TTCGATTCGGTTGGTTTATGTCATCGCG 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s TCGCCGTACCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 696s TCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s CGTTGGGGTTCGCCGTTCCCGG 696s CGTTGGGGTTCGCCGTTCCCGG 696s Processing line... 696s GTTGGGGTTCGCCG 696s GTTGGGGTTCGCCG 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s GTTCGCCGTACCCGGTGTGTCGTTGTAGGCCGTTGGG 696s GTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGG 696s Processing line... 696s Processing line... 696s Processing line... 696s CGCCGTTGAACG 696s CGCCGTTGAACG 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s Processing line... 696s TTTATGTCATCGCGCGGTTGTTTGG 696s TTTATGTCATCGCGCGGTTGTTTGG 696s Processing line... 696s Processing line... 696s Processing line... 696s TTGTAGGCCGTTG 696s TTGTAGGCCGTTG 696s Processing line... 696s --- Summary --- 696s Read 1 reference strings 696s Checked 21 alignments, 0 edits 696s --------------- 696s PASSED 696s ALSO checking that bowtie2 and bowtie2-align match up 696s /usr/bin/bowtie2 --n-ceil 0.096150684250895,0.0259442474717559 --large-index --cp-min 5 --cp-ival 3 --local -R 2 -i L,0.201754670892445 -N 0 --score-min L,8.33504230830753,1.30976214554616 --trim3 0 --rfg 39.4635097735554 --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 696s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 696s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 696s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (1) <= # seed mismatches (0) 696s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 696s Warning: skipping read 'R_1_1_1_172_172_1/1' because length (1) <= # seed mismatches (0) 696s Warning: skipping read 'R_1_1_1_172_172_1/1' because it was < 2 characters long 696s 179 reads; of these: 696s 179 (100.00%) were unpaired; of these: 696s 158 (88.27%) aligned 0 times 696s 15 (8.38%) aligned exactly 1 time 696s 6 (3.35%) aligned >1 times 696s 11.73% overall alignment rate 696s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 696s /usr/bin/bowtie2 --n-ceil 0.096150684250895,0.0259442474717559 --large-index --cp-min 5 --cp-ival 3 --local -R 2 -i L,0.201754670892445 -N 0 --score-min L,8.33504230830753,1.30976214554616 --trim3 0 --rfg 39.4635097735554 --qseq -p 4 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 696s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 696s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 696s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 696s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (1) <= # seed mismatches (0) 696s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 696s Warning: skipping read 'R_1_1_1_172_172_1/1' because length (1) <= # seed mismatches (0) 696s Warning: skipping read 'R_1_1_1_172_172_1/1' because it was < 2 characters long 696s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 696s 179 reads; of these: 696s 179 (100.00%) were unpaired; of these: 696s 158 (88.27%) aligned 0 times 696s 15 (8.38%) aligned exactly 1 time 696s 6 (3.35%) aligned >1 times 696s 11.73% overall alignment rate 696s Flattened IUPAC characters 696s Mutating sequence Sim.pm.2 696s Introducing 29 SNPs, 0/0 ref/read gaps, and 1 rearrangements 696s Finished SNPs 696s Finished ref gaps 696s Finished read gaps 696s Mutating sequence Sim.pm.1 696s Introducing 14 SNPs, 0/0 ref/read gaps, and 2 rearrangements 696s Finished SNPs 696s Finished ref gaps 696s Finished read gaps 696s Mutated reference genome to subject genome 696s SNPs introduced: 43 696s Reference gaps introduced: 0 696s Read gaps introduced: 0 696s Rearrangements introduced: 3 696s Created read sampler 696s Sampling 132 reads 696s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 696s *** Run 51 of 100 696s /usr/bin/bowtie2 --mp 6.60047750968514,4.35755002051208 -N 1 -L19 --nofw --trim3 8 --rfg 26.7183196442468 --cp-ival 1 -D 23 -k 9 --score-min L,4.08638853549167,6.67337065387355 --mm --np 20 --cp-min 8 --large-index -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 696s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 696s parsing sequence Sim.pm.1... 696s parsing sequence Sim.pm.2... 696s Parsed 234 reference bases 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 696s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 696s Warning: skipping read '1' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 696s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '5' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 696s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '7' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 696s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '12' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 696s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '16' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 696s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '17' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 696s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '21' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 696s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '25' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 696s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '30' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 696s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '32' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 696s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '38' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 696s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '42' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 696s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '45' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 696s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '49' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 696s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 696s Warning: skipping read '51' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 696s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (1) 696s Warning: skipping mate #1 of read '56' because it was < 2 characters long 696s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 696s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 697s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (1) 697s Warning: skipping mate #1 of read '64' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 697s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (1) 697s Warning: skipping mate #1 of read '65' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 697s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (1) 697s Warning: skipping mate #1 of read '70' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 697s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (1) 697s Warning: skipping mate #1 of read '75' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 697s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (1) 697s Warning: skipping mate #1 of read '78' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 697s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (1) 697s Warning: skipping mate #1 of read '82' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 697s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (1) 697s Warning: skipping mate #1 of read '83' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 697s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (1) 697s Warning: skipping mate #1 of read '91' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 697s Warning: skipping mate #2 of read '94' because length (1) <= # seed mismatches (1) 697s Warning: skipping mate #2 of read '94' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 697s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (1) 697s Warning: skipping mate #1 of read '99' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 697s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (1) 697s Warning: skipping mate #1 of read '102' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 697s Read 50 alignments... 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 697s Warning: skipping mate #2 of read '115' because length (1) <= # seed mismatches (1) 697s Warning: skipping mate #2 of read '115' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 697s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (1) 697s Warning: skipping mate #1 of read '120' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 697s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (1) 697s Warning: skipping mate #1 of read '127' because it was < 2 characters long 697s Read 100 alignments... 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 697s 132 reads; of these: 697s 114 (86.36%) were paired; of these: 697s 114 (100.00%) aligned concordantly 0 times 697s 0 (0.00%) aligned concordantly exactly 1 time 697s 0 (0.00%) aligned concordantly >1 times 697s ---- 697s 114 pairs aligned concordantly 0 times; of these: 697s 0 (0.00%) aligned discordantly 1 time 697s ---- 697s 114 pairs aligned 0 times concordantly or discordantly; of these: 697s 228 mates make up the pairs; of these: 697s 212 (92.98%) aligned 0 times 697s 4 (1.75%) aligned exactly 1 time 697s 12 (5.26%) aligned >1 times 697s 18 (13.64%) were unpaired; of these: 697s 18 (100.00%) aligned 0 times 697s 0 (0.00%) aligned exactly 1 time 697s 0 (0.00%) aligned >1 times 697s 6.50% overall alignment rate 697s Read 150 alignments... 697s Read 200 alignments... 697s Read 250 alignments... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GGTTCG 697s GGTTCG 697s Processing line... 697s GGTTCG 697s GGTTCG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CCAG 697s CCAG 697s Processing line... 697s CCAG 697s CCAG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CT 697s CT 697s Processing line... 697s CT 697s CT 697s Processing line... 697s CT 697s CT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GTCGT 697s GTCGT 697s Processing line... 697s GTCGT 697s GTCGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GTTCGATT 697s GTTCGATT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CGTTGTAGGCCGTT 697s CGTTGTAGGCCGTT 697s Processing line... 697s CGTTGTAGGCCGTT 697s CGTTGTAGGCCGTT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CGCCGTTCCCGGTGTGTCGT 697s CGCCGTTCCCGGTGTGTCGT 697s Processing line... 697s CGCCGTTCCCGGTGTGTCGT 697s CGCCGTTCCCGGTGTGTCGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TT 697s TT 697s Processing line... 697s TT 697s TT 697s Processing line... 697s TT 697s TT 697s Processing line... 697s TT 697s TT 697s Processing line... 697s TT 697s TT 697s Processing line... 697s TT 697s TT 697s Processing line... 697s TT 697s TT 697s Processing line... 697s TT 697s TT 697s Processing line... 697s TT 697s TT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CCG 697s CCG 697s Processing line... 697s CCG 697s CCG 697s Processing line... 697s CCG 697s CCG 697s Processing line... 697s CCG 697s CCG 697s Processing line... 697s CCG 697s CCG 697s Processing line... 697s CCG 697s CCG 697s Processing line... 697s CCG 697s CCG 697s Processing line... 697s CCG 697s CCG 697s Processing line... 697s CCG 697s CCG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TGCGG 697s TGCGG 697s Processing line... 697s TGCGG 697s TGCGG 697s Processing line... 697s Processing line... 697s TCC 697s TCC 697s Processing line... 697s TCC 697s TCC 697s Processing line... 697s TCC 697s TCC 697s Processing line... 697s TCC 697s TCC 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GGGTTC 697s GGGTTC 697s Processing line... 697s GGGTTC 697s GGGTTC 697s Processing line... 697s GGGTTC 697s GGGTTC 697s Processing line... 697s Processing line... 697s TCGCGCGG 697s TCGCGCGG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CCGTTC 697s CCGTTC 697s Processing line... 697s CCGTTC 697s CCGTTC 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GACG 697s GACG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s AGGCCGTTGGGGTTCGC 697s AGGCCGTTGGGGTTCGC 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s --- Summary --- 697s Read 1 reference strings 697s Checked 46 alignments, 0 edits 697s --------------- 697s PASSED 697s Flattened IUPAC characters 697s Mutating sequence Sim.pm.1 697s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 697s Finished SNPs 697s Finished ref gaps 697s Finished read gaps 697s Mutating sequence Sim.pm.2 697s Introducing 5 SNPs, 1/1 ref/read gaps, and 2 rearrangements 697s Finished SNPs 697s Finished ref gaps 697s Finished read gaps 697s Mutated reference genome to subject genome 697s SNPs introduced: 10 697s Reference gaps introduced: 2 697s Read gaps introduced: 1 697s *** Run 52 of 100 697s /usr/bin/bowtie2 --large-index --cp-min 4 --cp-ival 3 -D 25 -k 3 --mp 3.90249176449692,3.86149304976077 -R 2 --score-min L,8.93855128380324,6.68563629979225 --ma 9.99819810588231 --trim3 6 --rdg 34.1900151628774 -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta 697s Rearrangements introduced: 2 697s Created read sampler 697s Sampling 71 reads 697s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 697s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 697s parsing sequence Sim.pm.1... 697s parsing sequence Sim.pm.2... 697s Parsed 234 reference bases 697s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 697s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '4' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 697s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '11' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 697s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '15' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 697s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 697s Warning: skipping read '16' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 697s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '21' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 697s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 697s Warning: skipping read '33' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 697s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '35' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 697s Read 50 alignments... 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 697s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '55' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 697s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '58' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 697s 71 reads; of these: 697s 59 (83.10%) were paired; of these: 697s 59 (100.00%) aligned concordantly 0 times 697s 0 (0.00%) aligned concordantly exactly 1 time 697s 0 (0.00%) aligned concordantly >1 times 697s ---- 697s 59 pairs aligned concordantly 0 times; of these: 697s 1 (1.69%) aligned discordantly 1 time 697s ---- 697s 58 pairs aligned 0 times concordantly or discordantly; of these: 697s 116 mates make up the pairs; of these: 697s 93 (80.17%) aligned 0 times 697s 11 (9.48%) aligned exactly 1 time 697s 12 (10.34%) aligned >1 times 697s 12 (16.90%) were unpaired; of these: 697s 11 (91.67%) aligned 0 times 697s 0 (0.00%) aligned exactly 1 time 697s 1 (8.33%) aligned >1 times 697s 20.00% overall alignment rate 697s Read 100 alignments... 697s Read 150 alignments... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GTGTCGTTGTAGGCCGTTGGG 697s GTGTCGTTGTAGGCCGTTGGG 697s Processing line... 697s GTGTCGTTGTAGGCCGTTGGG 697s GTGTCGTTGTAGGCCGTTGGG 697s Processing line... 697s Processing line... 697s GTGTCGTTGTAG 697s GTGTCGTTGTAG 697s Processing line... 697s GTGTCGTTGTAG 697s GTGTCGTTGTAG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TGACG 697s TGACG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GTGTGTCGTTGTAGGCCGTTG 697s GTGTGTCGTTGTAGGCCGTTG 697s Processing line... 697s GTGTGTCGTTGTAGGCCGTTG 697s GTGTGTCGTTGTAGGCCGTTG 697s Processing line... 697s GTGTC 697s GTGTC 697s Processing line... 697s GTGTC 697s GTGTC 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GTCCCGCGGCC 697s GTCCCGCGGCC 697s Processing line... 697s Processing line... 697s GGGTTCGCCGTTCCC 697s GGGTTCGCCGTTCCC 697s Processing line... 697s GGGTTCGCCGTTCCC 697s GGGTTCGCCGTTCCC 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CATCGCGCGGTTGTTTGGTGT 697s CATCGCGCGGTTGTTTGGTGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GT 697s GT 697s Processing line... 697s GT 697s GT 697s Processing line... 697s GT 697s GT 697s Processing line... 697s Processing line... 697s TTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGT 697s TTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGT 697s Processing line... 697s TTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGT 697s TTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GGTGT 697s GGTGT 697s Processing line... 697s GGTGT 697s GGTGT 697s Processing line... 697s GGTGT 697s GGTGT 697s Processing line... 697s Processing line... 697s Processing line... 697s GGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGT 697s GGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GTGTCGTTGTAGGCCGTTGGG 697s GTGTCGTTGTAGGCCGTTGGG 697s Processing line... 697s GTGTCGTTGTAGGCCGTTGGG 697s GTGTCGTTGTAGGCCGTTGGG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TCTCAGGTT 697s TCTCAGGTT 697s Processing line... 697s Processing line... 697s GGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTAT 697s GGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTAT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTG 697s GGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTG 697s Processing line... 697s Processing line... 697s CTCAG 697s CTCAG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TGGTTTATG 697s TGGTTTATG 697s Processing line... 697s GCGCGGT 697s GCGCGGT 697s Processing line... 697s CGC 697s CGC 697s Processing line... 697s CGC 697s CGC 697s Processing line... 697s CGC 697s CGC 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TCGCCGTTCCCGGTGTGT 697s TCGCCGTTCCCGGTGTGT 697s Processing line... 697s TCGCCGTTCCCGGTGTGT 697s TCGCCGTTCCCGGTGTGT 697s Processing line... 697s Processing line... 697s GTGGGTGCG 697s GTGGGTGCG 697s Processing line... 697s Processing line... 697s Processing line... 697s CGGTGTGTCGTTGTAGGC 697s CGGTGTGTCGTTGTAGGC 697s Processing line... 697s CGGTGTGTCGTTGTAGGC 697s CGGTGTGTCGTTGTAGGC 697s Processing line... 697s Processing line... 697s GTGTCGT 697s GTGTCGT 697s Processing line... 697s GTGTCGT 697s GTGTCGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CCCGT 697s CCCGT 697s Processing line... 697s Processing line... 697s ATGTCATCGCGCGG 697s ATGTCATCGCGCGG 697s Processing line... 697s --- Summary --- 697s Read 1 reference strings 697s Checked 42 alignments, 0 edits 697s --------------- 697s PASSED 697s /usr/bin/bowtie2 --large-index --cp-min 4 --cp-ival 3 -D 25 -k 3 --mp 3.90249176449692,3.86149304976077 -R 2 --score-min L,8.93855128380324,6.68563629979225 --ma 9.99819810588231 --trim3 6 --rdg 34.1900151628774 -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 697s ALSO checking that bowtie2 and bowtie2-align match up 697s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 697s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '4' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 697s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '11' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 697s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '15' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 697s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 697s Warning: skipping read '16' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 697s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '21' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 697s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 697s Warning: skipping read '33' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 697s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '35' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 697s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '55' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 697s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '58' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 697s 71 reads; of these: 697s 59 (83.10%) were paired; of these: 697s 59 (100.00%) aligned concordantly 0 times 697s 0 (0.00%) aligned concordantly exactly 1 time 697s 0 (0.00%) aligned concordantly >1 times 697s ---- 697s 59 pairs aligned concordantly 0 times; of these: 697s 1 (1.69%) aligned discordantly 1 time 697s ---- 697s 58 pairs aligned 0 times concordantly or discordantly; of these: 697s 116 mates make up the pairs; of these: 697s 93 (80.17%) aligned 0 times 697s 11 (9.48%) aligned exactly 1 time 697s 12 (10.34%) aligned >1 times 697s 12 (16.90%) were unpaired; of these: 697s 11 (91.67%) aligned 0 times 697s 0 (0.00%) aligned exactly 1 time 697s 1 (8.33%) aligned >1 times 697s 20.00% overall alignment rate 697s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 697s /usr/bin/bowtie2 --large-index --cp-min 4 --cp-ival 3 -D 25 -k 3 --mp 3.90249176449692,3.86149304976077 -R 2 --score-min L,8.93855128380324,6.68563629979225 --ma 9.99819810588231 --trim3 6 --rdg 34.1900151628774 -f -p 4 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 697s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 697s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 697s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '4' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 697s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '11' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 697s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '15' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 697s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 697s Warning: skipping read '16' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 697s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '21' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 697s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 697s Warning: skipping read '33' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 697s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '35' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 697s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '55' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 697s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '58' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 697s 71 reads; of these: 697s 59 (83.10%) were paired; of these: 697s 59 (100.00%) aligned concordantly 0 times 697s 0 (0.00%) aligned concordantly exactly 1 time 697s 0 (0.00%) aligned concordantly >1 times 697s ---- 697s 59 pairs aligned concordantly 0 times; of these: 697s 1 (1.69%) aligned discordantly 1 time 697s ---- 697s 58 pairs aligned 0 times concordantly or discordantly; of these: 697s 116 mates make up the pairs; of these: 697s 93 (80.17%) aligned 0 times 697s 11 (9.48%) aligned exactly 1 time 697s 12 (10.34%) aligned >1 times 697s 12 (16.90%) were unpaired; of these: 697s 11 (91.67%) aligned 0 times 697s 0 (0.00%) aligned exactly 1 time 697s 1 (8.33%) aligned >1 times 697s 20.00% overall alignment rate 697s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 697s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 697s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 697s Flattened IUPAC characters 697s Mutating sequence Sim.pm.2 697s Introducing 23 SNPs, 0/2 ref/read gaps, and 1 rearrangements 697s Finished SNPs 697s Finished ref gaps 697s Finished read gaps 697s Mutating sequence Sim.pm.1 697s Introducing 14 SNPs, 1/2 ref/read gaps, and 1 rearrangements 697s Finished SNPs 697s Finished ref gaps 697s Finished read gaps 697s Mutated reference genome to subject genome 697s SNPs introduced: 37 697s Reference gaps introduced: 1 697s Read gaps introduced: 4 697s Rearrangements introduced: 2 697s Created read sampler 697s Sampling 81 reads 697s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 697s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 697s *** Run 53 of 100 697s /usr/bin/bowtie2 --rdg 36.2544937392846 --mm --score-min L,9.7974771893516,5.0618166258812 --ma 21.5980858396913 --trim3 3 --gbar 2 --cp-ival 1 --large-index --cp-min 4 --trim5 6 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 697s parsing sequence Sim.pm.1... 697s parsing sequence Sim.pm.2... 697s Parsed 234 reference bases 697s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 697s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '5' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 697s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '15' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 697s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '17' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 697s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '18' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 697s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 697s Warning: skipping read '24' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 697s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '25' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 697s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 697s Warning: skipping read '29' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 697s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '33' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 697s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 697s Warning: skipping read '40' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 697s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '47' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 697s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '49' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 697s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '51' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 697s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '55' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 697s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '58' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 697s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '60' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 697s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '66' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 697s Warning: skipping mate #2 of read '67' because length (1) <= # seed mismatches (0) 697s Warning: skipping mate #2 of read '67' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 697s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '70' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 697s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '71' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 697s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 697s Warning: skipping mate #1 of read '78' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 697s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 697s Warning: skipping read '79' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 697s Read 50 alignments... 697s Read 100 alignments... 697s 81 reads; of these: 697s 68 (83.95%) were paired; of these: 697s 68 (100.00%) aligned concordantly 0 times 697s 0 (0.00%) aligned concordantly exactly 1 time 697s 0 (0.00%) aligned concordantly >1 times 697s ---- 697s 68 pairs aligned concordantly 0 times; of these: 697s 0 (0.00%) aligned discordantly 1 time 697s ---- 697s 68 pairs aligned 0 times concordantly or discordantly; of these: 697s 136 mates make up the pairs; of these: 697s 122 (89.71%) aligned 0 times 697s 4 (2.94%) aligned exactly 1 time 697s 10 (7.35%) aligned >1 times 697s 13 (16.05%) were unpaired; of these: 697s 12 (92.31%) aligned 0 times 697s 1 (7.69%) aligned exactly 1 time 697s 0 (0.00%) aligned >1 times 697s 10.07% overall alignment rate 697s Read 150 alignments... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TTGGGGTTCGCCGTTC 697s TTGGGGTTCGCCGTTC 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s *** Run 54 of 100 697s /usr/bin/bowtie2 --rdg 11.431748804496 --mm --score-min L,6.10456040775759,2.89488223989727 --ma 26.8797429170358 --gbar 21 --large-index --cp-min 6 --cp-ival 1 -a --trim5 0 -f -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TT 697s TT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TGC 697s TGC 697s Processing line... 697s Processing line... 697s TAGGCCGTT 697s TAGGCCGTT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GGT 697s GGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CA 697s CA 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GTTGGTTT 697s GTTGGTTT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GGAGT 697s GGAGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GGTG 697s GGTG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TC 697s TC 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TTGGAGTCCCGCGGCCCG 697s TTGGAGTCCCGCGGCCCG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CCGCGGCCCGT 697s CCGCGGCCCGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TGAACG 697s TGAACG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TTCGCCGTT 697s TTCGCCGTT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TCCC 697s TCCC 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s --- Summary --- 697s Read 1 reference strings 697s Checked 15 alignments, 0 edits 697s --------------- 697s PASSED 697s Flattened IUPAC characters 697s Mutating sequence Sim.pm.2 697s Introducing 19 SNPs, 0/1 ref/read gaps, and 0 rearrangements 697s Finished SNPs 697s Finished ref gaps 697s Finished read gaps 697s Mutating sequence Sim.pm.1 697s Introducing 3 SNPs, 2/0 ref/read gaps, and 1 rearrangements 697s Finished SNPs 697s Finished ref gaps 697s Finished read gaps 697s Mutated reference genome to subject genome 697s SNPs introduced: 22 697s Reference gaps introduced: 2 697s Read gaps introduced: 1 697s Rearrangements introduced: 1 697s Created read sampler 697s Sampling 105 reads 697s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 697s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 697s parsing sequence Sim.pm.1... 697s parsing sequence Sim.pm.2... 697s Parsed 234 reference bases 697s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 697s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 697s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 697s Warning: skipping read '20' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 697s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 697s Warning: skipping read '37' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 697s Read 50 alignments... 697s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 697s Read 100 alignments... 697s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 697s 105 reads; of these: 697s 105 (100.00%) were unpaired; of these: 697s 71 (67.62%) aligned 0 times 697s 6 (5.71%) aligned exactly 1 time 697s 28 (26.67%) aligned >1 times 697s 32.38% overall alignment rate 697s Read 150 alignments... 697s Read 200 alignments... 697s Read 250 alignments... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CGTTCCCGGTGTGTCGTTGTAGGCCGT 697s CGTTCCCGGTGTGTCGTTGTAGGCCGT 697s Processing line... 697s CGTTCCCGGTGTGTCGTTGTAGGCCGT 697s CGTTCCCGGTGTGTCGTTGTAGGCCGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TCGTTGTAGGCCGTTGGGGTTCGCCGT 697s TCGTTGTAGGCCGTTGGGGTTCGCCGT 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s Processing line... 697s Processing line... 697s CGTTCCCGGTGTG 697s CGTTCCCGGTGTG 697s Processing line... 697s CGTTCCCGGTGTG 697s CGTTCCCGGTGTG 697s Processing line... 697s TTGTAGGC 697s TTGTAGGC 697s Processing line... 697s TTGTAGGC 697s TTGTAGGC 697s Processing line... 697s CGTT 697s CGTT 697s Processing line... 697s CGTT 697s CGTT 697s Processing line... 697s CGTT 697s CGTT 697s Processing line... 697s CGTT 697s CGTT 697s Processing line... 697s CGTT 697s CGTT 697s Processing line... 697s CGTT 697s CGTT 697s Processing line... 697s CGTT 697s CGTT 697s Processing line... 697s AACG 697s AACG 697s Processing line... 697s CGTT 697s CGTT 697s Processing line... 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s GTTG 697s GTTG 697s Processing line... 697s Processing line... 697s GTTCCCGGTGTGTCGTTGTAGGC 697s GTTCCCGGTGTGTCGTTGTAGGC 697s Processing line... 697s GTTCCCGGTGTGTCGTTGTAGGC 697s GTTCCCGGTGTGTCGTTGTAGGC 697s Processing line... 697s Processing line... 697s GGTTCGCCGTTCCCGGTGT 697s GGTTCGCCGTTCCCGGTGT 697s Processing line... 697s GGTTCGCCGTTCCCGGTGT 697s GGTTCGCCGTTCCCGGTGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GGGTTCGCCGTTCCCG 697s GGGTTCGCCGTTCCCG 697s Processing line... 697s GGGTTCGCCGTTCCCG 697s GGGTTCGCCGTTCCCG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GGTGACGCCGT 697s GGTGACGCCGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 697s CCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 697s Processing line... 697s CCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 697s CCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 697s Processing line... 697s GGTTCGCCGTTCCCGGTGTGTCG 697s GGTTCGCCGTTCCCGGTGTGTCG 697s Processing line... 697s GGTTCGCCGTTCCCGGTGTGTCG 697s GGTTCGCCGTTCCCGGTGTGTCG 697s Processing line... 697s GCCGTT 697s GCCGTT 697s Processing line... 697s GCCGTT 697s GCCGTT 697s Processing line... 697s GCCGTT 697s GCCGTT 697s Processing line... 697s GCCGTT 697s GCCGTT 697s Processing line... 697s GCCGTT 697s GCCGTT 697s Processing line... 697s Processing line... 697s Processing line... 697s GGTTCGCCGTTCCCGGTGTGTCG 697s GGTTCGCCGTTCCCGGTGTGTCG 697s Processing line... 697s GGTTCGCCGTTCCCGGTGTGTCG 697s GGTTCGCCGTTCCCGGTGTGTCG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s CGGTG 697s CGGTG 697s Processing line... 697s CGGTG 697s CGGTG 697s Processing line... 697s Processing line... 697s CAT 697s CAT 697s Processing line... 697s ATG 697s ATG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s AAC 697s AAC 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s GTT 697s GTT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s CC 697s CC 697s Processing line... 697s CC 697s CC 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s CC 697s CC 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s CC 697s CC 697s Processing line... 697s CC 697s CC 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s CC 697s CC 697s Processing line... 697s CC 697s CC 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s CC 697s CC 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s CC 697s CC 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s CC 697s CC 697s Processing line... 697s CC 697s CC 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s CC 697s CC 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s CC 697s CC 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s CC 697s CC 697s Processing line... 697s CC 697s CC 697s Processing line... 697s CC 697s CC 697s Processing line... 697s GG 697s GG 697s Processing line... 697s CC 697s CC 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GG 697s GG 697s Processing line... 697s GTCGTTGTAGG 697s GTCGTTGTAGG 697s Processing line... 697s GTCGTTGTAGG 697s GTCGTTGTAGG 697s Processing line... 697s CGTTCCCGGT 697s CGTTCCCGGT 697s Processing line... 697s CGTTCCCGGT 697s CGTTCCCGGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TGGGGT 697s TGGGGT 697s Processing line... 697s TGGGGT 697s TGGGGT 697s Processing line... 697s TGGGGT 697s TGGGGT 697s Processing line... 697s GGTGCGGCG 697s GGTGCGGCG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TGTCGTTGTAGGCCGT 697s TGTCGTTGTAGGCCGT 697s Processing line... 697s TGTCGTTGTAGGCCGT 697s TGTCGTTGTAGGCCGT 697s Processing line... 697s TTCGCCGTTCC 697s TTCGCCGTTCC 697s Processing line... 697s TTCGCCGTTCC 697s TTCGCCGTTCC 697s Processing line... 697s AGGCC 697s AGGCC 697s Processing line... 697s AGGCC 697s AGGCC 697s Processing line... 697s GGGGT 697s GGGGT 697s Processing line... 697s GGGGT 697s GGGGT 697s Processing line... 697s GGGGT 697s GGGGT 697s Processing line... 697s GGGGT 697s GGGGT 697s Processing line... 697s CGCGGTTGTT 697s CGCGGTTGTT 697s Processing line... 697s Processing line... 697s Processing line... 697s TTG 697s TTG 697s Processing line... 697s TTG 697s TTG 697s Processing line... 697s TTG 697s TTG 697s Processing line... 697s TTG 697s TTG 697s Processing line... 697s TTG 697s TTG 697s Processing line... 697s TTG 697s TTG 697s Processing line... 697s TTG 697s TTG 697s Processing line... 697s TTG 697s TTG 697s Processing line... 697s TTG 697s TTG 697s Processing line... 697s TTG 697s TTG 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s TGTG 697s TGTG 697s Processing line... 697s TGTG 697s TGTG 697s Processing line... 697s TGTG 697s TGTG 697s Processing line... 697s TGTGTCGTTGTAGGC 697s TGTGTCGTTGTAGGC 697s Processing line... 697s TGTGTCGTTGTAGGC 697s TGTGTCGTTGTAGGC 697s Processing line... 697s GGCCAGTTCGATTCGGTTGGTTTATGTCATCGCG 697s GGCCAGTTCGATTCGGTTGGTTTATGTCATCGCG 697s Processing line... 697s Processing line... 697s Processing line... 697s CCCGT 697s CCCGT 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s --- Summary --- 697s Read 1 reference strings 697s Checked 178 alignments, 0 edits 697s --------------- 697s PASSED 697s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 697s /usr/bin/bowtie2 --rdg 11.431748804496 --mm --score-min L,6.10456040775759,2.89488223989727 --ma 26.8797429170358 --gbar 21 --large-index --cp-min 6 --cp-ival 1 -a --trim5 0 -f -p 4 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 697s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 697s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 697s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 697s Warning: skipping read '20' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 697s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 697s Warning: skipping read '37' because it was < 2 characters long 697s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 697s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 697s 105 reads; of these: 697s 105 (100.00%) were unpaired; of these: 697s 71 (67.62%) aligned 0 times 697s 6 (5.71%) aligned exactly 1 time 697s 28 (26.67%) aligned >1 times 697s 32.38% overall alignment rate 697s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 697s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 697s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 697s Flattened IUPAC characters 697s Mutating sequence Sim.pm.1 697s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 697s Finished SNPs 697s Finished ref gaps 697s Finished read gaps 697s Mutating sequence Sim.pm.2 697s Introducing 19 SNPs, 0/3 ref/read gaps, and 0 rearrangements 697s Finished SNPs 697s Finished ref gaps 697s Finished read gaps 697s Mutated reference genome to subject genome 697s SNPs introduced: 20 697s Reference gaps introduced: 1 697s Read gaps introduced: 3 697s Rearrangements introduced: 0 697s Created read sampler 697s Sampling 142 reads 697s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 697s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 697s parsing sequence Sim.pm.1... 697s *** Run 55 of 100 697s /usr/bin/bowtie2 --mp 3.9510521589962,3.61805384305053 --trim5 4 -M 3 --cp-ival 1 --local -R 4 --score-min L,7.47292786799319,9.8490891080222 --mm --np 1 --cp-min 3 --large-index --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq 697s parsing sequence Sim.pm.2... 697s Parsed 234 reference bases 697s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 697s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 697s Read 50 alignments... 697s 142 reads; of these: 697s 142 (100.00%) were unpaired; of these: 697s 142 (100.00%) aligned 0 times 697s 0 (0.00%) aligned exactly 1 time 697s 0 (0.00%) aligned >1 times 697s 0.00% overall alignment rate 697s Read 100 alignments... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s Processing line... 697s --- Summary --- 697s Read 1 reference strings 697s Checked 0 alignments, 0 edits 697s --------------- 697s PASSED 697s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 697s /usr/bin/bowtie2 --mp 3.9510521589962,3.61805384305053 --trim5 4 -M 3 --cp-ival 1 --local -R 4 --score-min L,7.47292786799319,9.8490891080222 --mm --np 1 --cp-min 3 --large-index --qseq -p 3 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 697s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 697s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 697s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 697s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 697s 142 reads; of these: 697s 142 (100.00%) were unpaired; of these: 697s 142 (100.00%) aligned 0 times 697s 0 (0.00%) aligned exactly 1 time 697s 0 (0.00%) aligned >1 times 697s 0.00% overall alignment rate 697s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 697s Flattened IUPAC characters 697s Mutating sequence Sim.pm.1 697s Introducing 17 SNPs, 0/1 ref/read gaps, and 0 rearrangements 697s Finished SNPs 697s Finished ref gaps 697s Finished read gaps 697s Mutating sequence Sim.pm.2 697s Introducing 19 SNPs, 0/1 ref/read gaps, and 1 rearrangements 697s Finished SNPs 697s Finished ref gaps 697s Finished read gaps 697s Mutated reference genome to subject genome 697s SNPs introduced: 36 697s Reference gaps introduced: 0 697s Read gaps introduced: 2 697s Rearrangements introduced: 1 697s Created read sampler 697s Sampling 125 reads 697s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 697s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 697s parsing sequence Sim.pm.1... 697s parsing sequence Sim.pm.2... 697s Parsed 234 reference bases 697s *** Run 56 of 100 697s /usr/bin/bowtie2 --score-min L,5.58942239829381,3.19568683795323 -i C,1.54554559913062 --mp 6.39946329079307,2.97138196209793 --rdg 18.7388567523113 --mm --cp-min 12 -a --large-index --trim5 8 --local --cp-ival 1 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq 698s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 698s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 698s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 698s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 698s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 698s Warning: skipping mate #2 of read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 698s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 698s Warning: skipping mate #2 of read 'R_1_1_1_100_100_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 698s Warning: skipping mate #2 of read 'R_1_1_1_104_104_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 698s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 698s Read 50 alignments... 698s Read 100 alignments... 698s Read 150 alignments... 698s 125 reads; of these: 698s 96 (76.80%) were paired; of these: 698s 96 (100.00%) aligned concordantly 0 times 698s 0 (0.00%) aligned concordantly exactly 1 time 698s 0 (0.00%) aligned concordantly >1 times 698s ---- 698s 96 pairs aligned concordantly 0 times; of these: 698s 0 (0.00%) aligned discordantly 1 time 698s ---- 698s 96 pairs aligned 0 times concordantly or discordantly; of these: 698s 192 mates make up the pairs; of these: 698s 192 (100.00%) aligned 0 times 698s 0 (0.00%) aligned exactly 1 time 698s 0 (0.00%) aligned >1 times 698s 29 (23.20%) were unpaired; of these: 698s 29 (100.00%) aligned 0 times 698s 0 (0.00%) aligned exactly 1 time 698s 0 (0.00%) aligned >1 times 698s 0.00% overall alignment rate 698s Read 200 alignments... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s /usr/bin/bowtie2 --score-min L,5.58942239829381,3.19568683795323 -i C,1.54554559913062 --mp 6.39946329079307,2.97138196209793 --rdg 18.7388567523113 --mm --cp-min 12 -a --large-index --trim5 8 --local --cp-ival 1 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s --- Summary --- 698s Read 1 reference strings 698s Checked 0 alignments, 0 edits 698s --------------- 698s PASSED 698s ALSO checking that bowtie2 and bowtie2-align match up 698s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 698s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 698s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 698s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 698s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 698s Warning: skipping mate #2 of read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 698s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 698s Warning: skipping mate #2 of read 'R_1_1_1_100_100_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 698s Warning: skipping mate #2 of read 'R_1_1_1_104_104_1/1' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 698s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 698s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 698s 125 reads; of these: 698s 96 (76.80%) were paired; of these: 698s 96 (100.00%) aligned concordantly 0 times 698s 0 (0.00%) aligned concordantly exactly 1 time 698s 0 (0.00%) aligned concordantly >1 times 698s ---- 698s 96 pairs aligned concordantly 0 times; of these: 698s 0 (0.00%) aligned discordantly 1 time 698s ---- 698s 96 pairs aligned 0 times concordantly or discordantly; of these: 698s 192 mates make up the pairs; of these: 698s 192 (100.00%) aligned 0 times 698s 0 (0.00%) aligned exactly 1 time 698s 0 (0.00%) aligned >1 times 698s 29 (23.20%) were unpaired; of these: 698s 29 (100.00%) aligned 0 times 698s 0 (0.00%) aligned exactly 1 time 698s 0 (0.00%) aligned >1 times 698s 0.00% overall alignment rate 698s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 698s Flattened IUPAC characters 698s Mutating sequence Sim.pm.2 698s Introducing 20 SNPs, 0/1 ref/read gaps, and 1 rearrangements 698s Finished SNPs 698s Finished ref gaps 698s Finished read gaps 698s Mutating sequence Sim.pm.1 698s Introducing 13 SNPs, 1/1 ref/read gaps, and 1 rearrangements 698s Finished SNPs 698s Finished ref gaps 698s Finished read gaps 698s Mutated reference genome to subject genome 698s SNPs introduced: 33 698s Reference gaps introduced: 1 698s Read gaps introduced: 2 698s Rearrangements introduced: 2 698s Created read sampler 698s Sampling 125 reads 698s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 698s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 698s parsing sequence Sim.pm.1... 698s *** Run 57 of 100 698s /usr/bin/bowtie2 --large-index --np 6 --cp-min 3 -D 33 --score-min L,6.54129946884255,1.92123380364146 --ma 37.8449385579768 --rdg 35.422715031044,19.7211952988532 --norc --cp-ival 3 --mp 4.8629539745632,2.5997513690865 -N 0 -L19 --trim3 1 --rfg 17.2756766664947,9.93387710367309 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 698s parsing sequence Sim.pm.2... 698s Parsed 234 reference bases 698s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 698s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '3' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 698s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '11' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 698s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read '42' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 698s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '44' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 698s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read '71' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 698s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '77' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 698s Read 50 alignments... 698s Read 100 alignments... 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 698s Read 150 alignments... 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 698s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '113' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 698s Warning: skipping mate #2 of read '116' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read '116' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 698s 125 reads; of these: 698s 123 (98.40%) were paired; of these: 698s 122 (99.19%) aligned concordantly 0 times 698s 0 (0.00%) aligned concordantly exactly 1 time 698s 1 (0.81%) aligned concordantly >1 times 698s ---- 698s 122 pairs aligned concordantly 0 times; of these: 698s 1 (0.82%) aligned discordantly 1 time 698s ---- 698s 121 pairs aligned 0 times concordantly or discordantly; of these: 698s 242 mates make up the pairs; of these: 698s 219 (90.50%) aligned 0 times 698s 8 (3.31%) aligned exactly 1 time 698s 15 (6.20%) aligned >1 times 698s 2 (1.60%) were unpaired; of these: 698s 2 (100.00%) aligned 0 times 698s 0 (0.00%) aligned exactly 1 time 698s 0 (0.00%) aligned >1 times 698s 10.89% overall alignment rate 698s Read 200 alignments... 698s Read 250 alignments... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s CGTT 698s CGTT 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s CT 698s CT 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GGC 698s GGC 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s TGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCG 698s TGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s AAC 698s AAC 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s ACG 698s ACG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GCG 698s GCG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GG 698s GG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s CCA 698s CCA 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GG 698s GG 698s Processing line... 698s GC 698s GC 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTC 698s GTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTC 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s ACGC 698s ACGC 698s Processing line... 698s TGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGC 698s TGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGC 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GAC 698s GAC 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s TTTATGTCATCGCGCGGTTGT 698s TTTATGTCATCGCGCGGTTGT 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s TGTAGGCCGTTGGGGTTC 698s TGTAGGCCGTTGGGGTTC 698s Processing line... 698s Processing line... 698s AGGCCGTTG 698s AGGCCGTTG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s AC 698s AC 698s Processing line... 698s Processing line... 698s TGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 698s TGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GTTCCC 698s GTTCCC 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GTCG 698s GTCG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s TAT 698s TAT 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GGT 698s GGT 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s AGGCCGTTGGGGTTCGCCG 698s AGGCCGTTGGGGTTCGCCG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GTGA 698s GTGA 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s CGT 698s CGT 698s Processing line... 698s --- Summary --- 698s Read 1 reference strings 698s Checked 27 alignments, 0 edits 698s --------------- 698s PASSED 698s Flattened IUPAC characters 698s Mutating sequence Sim.pm.1 698s Introducing 6 SNPs, 1/1 ref/read gaps, and 0 rearrangements 698s Finished SNPs 698s Finished ref gaps 698s Finished read gaps 698s Mutating sequence Sim.pm.2 698s Introducing 18 SNPs, 0/1 ref/read gaps, and 2 rearrangements 698s Finished SNPs 698s Finished ref gaps 698s Finished read gaps 698s Mutated reference genome to subject genome 698s SNPs introduced: 24 698s Reference gaps introduced: 1 698s Read gaps introduced: 2 698s Rearrangements introduced: 2 698s Created read sampler 698s Sampling 193 reads 698s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 698s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 698s parsing sequence Sim.pm.1... 698s parsing sequence Sim.pm.2... 698s Parsed 234 reference bases 698s *** Run 58 of 100 698s /usr/bin/bowtie2 --score-min L,4.75327859028647,5.70964968126278 --ma 22.4771470835235 --rdg 19.9236501802272,10.3769092410976 --mm --large-index --cp-min 7 --trim3 4 --mp 7.22419256393629,3.94048341267793 --rfg 9.96014423650329,2.40717153558954 -M 4 --norc --cp-ival 1 -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta 698s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 698s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 698s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '16' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 698s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '31' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 698s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '32' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 698s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '40' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 698s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '41' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 698s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '53' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 698s Read 50 alignments... 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 698s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '70' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 698s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '73' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 698s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read '75' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 698s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '85' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 698s Warning: skipping mate #2 of read '90' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read '90' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 698s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '94' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 698s Warning: skipping mate #2 of read '95' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read '95' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 698s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '101' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 698s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '104' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 698s Warning: skipping mate #2 of read '111' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read '111' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 698s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '112' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 698s Read 100 alignments... 698s Read 150 alignments... 698s Read 200 alignments... 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 698s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '119' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 698s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '122' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 698s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '124' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 698s Warning: skipping mate #1 of read '135' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '135' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 698s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '151' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 698s Warning: skipping mate #1 of read '156' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '156' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 698s Warning: skipping mate #1 of read '158' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '158' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 698s Read 250 alignments... 698s Read 300 alignments... 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 698s Warning: skipping mate #1 of read '163' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '163' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 698s Warning: skipping mate #1 of read '171' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '171' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 698s Warning: skipping mate #2 of read '179' because length (1) <= # seed mismatches (0) 698s Warning: skipping mate #2 of read '179' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 698s Warning: skipping mate #1 of read '184' because length (0) <= # seed mismatches (0) 698s Warning: skipping mate #1 of read '184' because it was < 2 characters long 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for read '191; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 698s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 698s 193 reads; of these: 698s 179 (92.75%) were paired; of these: 698s 179 (100.00%) aligned concordantly 0 times 698s 0 (0.00%) aligned concordantly exactly 1 time 698s 0 (0.00%) aligned concordantly >1 times 698s ---- 698s 179 pairs aligned concordantly 0 times; of these: 698s 0 (0.00%) aligned discordantly 1 time 698s ---- 698s 179 pairs aligned 0 times concordantly or discordantly; of these: 698s 358 mates make up the pairs; of these: 698s 322 (89.94%) aligned 0 times 698s 14 (3.91%) aligned exactly 1 time 698s 22 (6.15%) aligned >1 times 698s 14 (7.25%) were unpaired; of these: 698s 14 (100.00%) aligned 0 times 698s 0 (0.00%) aligned exactly 1 time 698s 0 (0.00%) aligned >1 times 698s 9.68% overall alignment rate 698s Read 350 alignments... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GTAGGCC 698s GTAGGCC 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GAGTCCCGCGGCC 698s GAGTCCCGCGGCC 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GGTGTGTC 698s GGTGTGTC 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s AG 698s AG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s TCGTTG 698s TCGTTG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GA 698s GA 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GCGGGG 698s GCGGGG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGG 698s GTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GTGTGTCGTTGTAGGCCG 698s GTGTGTCGTTGTAGGCCG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GC 698s GC 698s Processing line... 698s Processing line... 698s AGGCCGTTGGGGTTCGCCGTTCCCGGTGT 698s AGGCCGTTGGGGTTCGCCGTTCCCGGTGT 698s Processing line... 698s Processing line... 698s ACGTGCG 698s ACGTGCG 698s Processing line... 698s Processing line... 698s TG 698s TG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GGT 698s GGT 698s Processing line... 698s Processing line... 698s GTGTC 698s GTGTC 698s Processing line... 698s Processing line... 698s CGGGGGTCTCAGGTTGGAG 698s CGGGGGTCTCAGGTTGGAG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s CTGGTGACG 698s CTGGTGACG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s CG 698s CG 698s Processing line... 698s Processing line... 698s GCGT 698s GCGT 698s Processing line... 698s Processing line... 698s ACGCCGTTGAACGTGCGG 698s ACGCCGTTGAACGTGCGG 698s Processing line... 698s Processing line... 698s TCT 698s TCT 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GTTGGGGTTCGCCGTTCCCGGTGTGT 698s GTTGGGGTTCGCCGTTCCCGGTGTGT 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s CA 698s CA 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GGGTC 698s GGGTC 698s Processing line... 698s Processing line... 698s Processing line... 698s CGGG 698s CGGG 698s Processing line... 698s Processing line... 698s AA 698s AA 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTAT 698s GTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTAT 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GGCCCG 698s GGCCCG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GA 698s GA 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GTT 698s GTT 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s CA 698s CA 698s Processing line... 698s Processing line... 698s TCCCG 698s TCCCG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s CG 698s CG 698s Processing line... 698s Processing line... 698s TGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTT 698s TGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTT 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s GGTTCGCCGTTCCCG 698s GGTTCGCCGTTCCCG 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s AC 698s AC 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s --- Summary --- 698s Read 1 reference strings 698s Checked 36 alignments, 0 edits 698s --------------- 698s PASSED 698s Flattened IUPAC characters 698s Mutating sequence Sim.pm.2 698s Introducing 8 SNPs, 0/0 ref/read gaps, and 2 rearrangements 698s Finished SNPs 698s Finished ref gaps 698s Finished read gaps 698s Mutating sequence Sim.pm.1 698s Introducing 20 SNPs, 0/0 ref/read gaps, and 0 rearrangements 698s Finished SNPs 698s Finished ref gaps 698s Finished read gaps 698s Mutated reference genome to subject genome 698s SNPs introduced: 28 698s Reference gaps introduced: 0 698s Read gaps introduced: 0 698s Rearrangements introduced: 2 698s Created read sampler 698s Sampling 84 reads 698s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 698s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 698s parsing sequence Sim.pm.1... 698s parsing sequence Sim.pm.2... 698s Parsed 234 reference bases 698s *** Run 59 of 100 698s /usr/bin/bowtie2 --large-index --cp-min 3 -D 20 --score-min L,8.35899459082379,5.58785449199734 --mm --rdg 36.0598799707786 --trim5 9 -M 2 --cp-ival 2 --local --mp 4.80637391728432,3.60478006368797 --trim3 3 --rfg 28.9797188515198,14.3620983226124 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 698s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 698s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '4' because it was < 2 characters long 698s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 698s Warning: skipping read '7' because it was < 2 characters long 698s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '10' because it was < 2 characters long 698s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '11' because it was < 2 characters long 698s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '26' because it was < 2 characters long 698s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '29' because it was < 2 characters long 698s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '31' because it was < 2 characters long 698s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '34' because it was < 2 characters long 698s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '35' because it was < 2 characters long 698s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 698s Warning: skipping read '40' because it was < 2 characters long 698s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '42' because it was < 2 characters long 698s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '43' because it was < 2 characters long 698s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '46' because it was < 2 characters long 698s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '54' because it was < 2 characters long 698s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '55' because it was < 2 characters long 698s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '56' because it was < 2 characters long 698s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '59' because it was < 2 characters long 698s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '63' because it was < 2 characters long 698s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '67' because it was < 2 characters long 698s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '73' because it was < 2 characters long 698s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 698s Warning: skipping read '83' because it was < 2 characters long 698s 84 reads; of these: 698s 84 (100.00%) were unpaired; of these: 698s 84 (100.00%) aligned 0 times 698s 0 (0.00%) aligned exactly 1 time 698s 0 (0.00%) aligned >1 times 698s 0.00% overall alignment rate 698s Read 50 alignments... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s Processing line... 698s --- Summary --- 698s Read 1 reference strings 698s Checked 0 alignments, 0 edits 698s --------------- 698s PASSED 698s Flattened IUPAC characters 698s Mutating sequence Sim.pm.2 698s Introducing 7 SNPs, 1/1 ref/read gaps, and 0 rearrangements 698s Finished SNPs 698s Finished ref gaps 698s Finished read gaps 698s Mutating sequence Sim.pm.1 698s Introducing 11 SNPs, 1/0 ref/read gaps, and 1 rearrangements 698s Finished SNPs 698s Finished ref gaps 698s Finished read gaps 698s Mutated reference genome to subject genome 698s SNPs introduced: 18 698s Reference gaps introduced: 2 698s Read gaps introduced: 1 698s Rearrangements introduced: 1 698s Created read sampler 698s Sampling 34 reads 698s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 698s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 698s parsing sequence Sim.pm.1... 698s parsing sequence Sim.pm.2... 698s Parsed 234 reference bases 698s *** Run 60 of 100 698s /usr/bin/bowtie2 --rfg 6.83716037969973,2.94919617366124 -i L,0.230723066307353,0.812974755234483 --mp 3.75999279161887,3.05907194876164 --cp-ival 1 --local --trim5 8 --n-ceil 1.48652790200658,0.434217043411196 --mm -R 3 --score-min L,6.18587417984349,5.109193566852 --large-index --np 4 --cp-min 13 -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta 699s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '1' because it was < 2 characters long 699s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 699s Warning: skipping read '3' because it was < 2 characters long 699s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '9' because it was < 2 characters long 699s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '11' because it was < 2 characters long 699s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '21' because it was < 2 characters long 699s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '25' because it was < 2 characters long 699s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '27' because it was < 2 characters long 699s 34 reads; of these: 699s 21 (61.76%) were paired; of these: 699s 21 (100.00%) aligned concordantly 0 times 699s 0 (0.00%) aligned concordantly exactly 1 time 699s 0 (0.00%) aligned concordantly >1 times 699s ---- 699s 21 pairs aligned concordantly 0 times; of these: 699s 0 (0.00%) aligned discordantly 1 time 699s ---- 699s 21 pairs aligned 0 times concordantly or discordantly; of these: 699s 42 mates make up the pairs; of these: 699s 42 (100.00%) aligned 0 times 699s 0 (0.00%) aligned exactly 1 time 699s 0 (0.00%) aligned >1 times 699s 13 (38.24%) were unpaired; of these: 699s 13 (100.00%) aligned 0 times 699s 0 (0.00%) aligned exactly 1 time 699s 0 (0.00%) aligned >1 times 699s 0.00% overall alignment rate 699s Read 50 alignments... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s --- Summary --- 699s Read 1 reference strings 699s Checked 0 alignments, 0 edits 699s --------------- 699s PASSED 699s ALSO checking that bowtie2 and bowtie2-align match up 699s /usr/bin/bowtie2 --rfg 6.83716037969973,2.94919617366124 -i L,0.230723066307353,0.812974755234483 --mp 3.75999279161887,3.05907194876164 --cp-ival 1 --local --trim5 8 --n-ceil 1.48652790200658,0.434217043411196 --mm -R 3 --score-min L,6.18587417984349,5.109193566852 --large-index --np 4 --cp-min 13 -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 699s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '1' because it was < 2 characters long 699s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 699s Warning: skipping read '3' because it was < 2 characters long 699s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '9' because it was < 2 characters long 699s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '11' because it was < 2 characters long 699s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '21' because it was < 2 characters long 699s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '25' because it was < 2 characters long 699s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '27' because it was < 2 characters long 699s 34 reads; of these: 699s 21 (61.76%) were paired; of these: 699s 21 (100.00%) aligned concordantly 0 times 699s 0 (0.00%) aligned concordantly exactly 1 time 699s 0 (0.00%) aligned concordantly >1 times 699s ---- 699s 21 pairs aligned concordantly 0 times; of these: 699s 0 (0.00%) aligned discordantly 1 time 699s ---- 699s 21 pairs aligned 0 times concordantly or discordantly; of these: 699s 42 mates make up the pairs; of these: 699s 42 (100.00%) aligned 0 times 699s 0 (0.00%) aligned exactly 1 time 699s 0 (0.00%) aligned >1 times 699s 13 (38.24%) were unpaired; of these: 699s 13 (100.00%) aligned 0 times 699s 0 (0.00%) aligned exactly 1 time 699s 0 (0.00%) aligned >1 times 699s 0.00% overall alignment rate 699s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 699s Flattened IUPAC characters 699s Mutating sequence Sim.pm.1 699s Introducing 14 SNPs, 0/0 ref/read gaps, and 0 rearrangements 699s Finished SNPs 699s Finished ref gaps 699s Finished read gaps 699s Mutating sequence Sim.pm.2 699s Introducing 18 SNPs, 1/2 ref/read gaps, and 1 rearrangements 699s Finished SNPs 699s Finished ref gaps 699s Finished read gaps 699s Mutated reference genome to subject genome 699s SNPs introduced: 32 699s Reference gaps introduced: 1 699s Read gaps introduced: 2 699s Rearrangements introduced: 1 699s Created read sampler 699s Sampling 148 reads 699s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 699s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 699s parsing sequence Sim.pm.1... 699s parsing sequence Sim.pm.2... 699s Parsed 234 reference bases 699s *** Run 61 of 100 699s /usr/bin/bowtie2 --cp-ival 1 --rfg 40.2589505109986,14.4367278679842 --nofw --cp-min 2 --np 10 --large-index --rdg 47.1764003117541 --mm --ma 8.42062695080102 --score-min L,4.2088035120388,2.81950089412629 -R 3 -k 2 -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw 699s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 699s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 699s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 699s Warning: skipping read '55' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 699s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 699s Warning: skipping read '86' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 699s Warning: skipping read '129' because length (1) <= # seed mismatches (0) 699s Warning: skipping read '129' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 699s Read 50 alignments... 699s Read 100 alignments... 699s 148 reads; of these: 699s 148 (100.00%) were unpaired; of these: 699s 129 (87.16%) aligned 0 times 699s 7 (4.73%) aligned exactly 1 time 699s 12 (8.11%) aligned >1 times 699s 12.84% overall alignment rate 699s Read 150 alignments... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CC 699s CC 699s Processing line... 699s CC 699s CC 699s Processing line... 699s GTCC 699s GTCC 699s Processing line... 699s GCCGTT 699s GCCGTT 699s Processing line... 699s GCCGTT 699s GCCGTT 699s Processing line... 699s Processing line... 699s Processing line... 699s GGCCC 699s GGCCC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTCC 699s GTCC 699s Processing line... 699s CGCCGTTGA 699s CGCCGTTGA 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TGTC 699s TGTC 699s Processing line... 699s TGTC 699s TGTC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CCCGGTGTGTC 699s CCCGGTGTGTC 699s Processing line... 699s CCCGGTGTGTC 699s CCCGGTGTGTC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TTGGGGTTCGCCGTTCCCGGTGTGTC 699s TTGGGGTTCGCCGTTCCCGGTGTGTC 699s Processing line... 699s TTGGGGTTCGCCGTTCCCGGTGTGTC 699s TTGGGGTTCGCCGTTCCCGGTGTGTC 699s Processing line... 699s Processing line... 699s GTTGTA 699s GTTGTA 699s Processing line... 699s GTTGTA 699s GTTGTA 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TGACGCCGTTG 699s TGACGCCGTTG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CGT 699s CGT 699s Processing line... 699s CGT 699s CGT 699s Processing line... 699s Processing line... 699s Processing line... 699s CGTGG 699s CGTGG 699s Processing line... 699s AGTC 699s AGTC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GGT 699s GGT 699s Processing line... 699s GGT 699s GGT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 699s CCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 699s Processing line... 699s CCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 699s CCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTTC 699s GTTC 699s Processing line... 699s GTTC 699s GTTC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GA 699s GA 699s Processing line... 699s GA 699s GA 699s Processing line... 699s Processing line... 699s CG 699s CG 699s Processing line... 699s CG 699s CG 699s Processing line... 699s --- Summary --- 699s Read 1 reference strings 699s Checked 31 alignments, 0 edits 699s --------------- 699s PASSED 699s ALSO checking that bowtie2 and bowtie2-align match up 699s /usr/bin/bowtie2 --cp-ival 1 --rfg 40.2589505109986,14.4367278679842 --nofw --cp-min 2 --np 10 --large-index --rdg 47.1764003117541 --mm --ma 8.42062695080102 --score-min L,4.2088035120388,2.81950089412629 -R 3 -k 2 -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 699s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 699s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 699s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 699s Warning: skipping read '55' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 699s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 699s Warning: skipping read '86' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 699s Warning: skipping read '129' because length (1) <= # seed mismatches (0) 699s Warning: skipping read '129' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 699s 148 reads; of these: 699s 148 (100.00%) were unpaired; of these: 699s 129 (87.16%) aligned 0 times 699s 7 (4.73%) aligned exactly 1 time 699s 12 (8.11%) aligned >1 times 699s 12.84% overall alignment rate 699s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 699s /usr/bin/bowtie2 --cp-ival 1 --rfg 40.2589505109986,14.4367278679842 --nofw --cp-min 2 --np 10 --large-index --rdg 47.1764003117541 --mm --ma 8.42062695080102 --score-min L,4.2088035120388,2.81950089412629 -R 3 -k 2 -r -p 4 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 699s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 699s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 699s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 699s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 699s Warning: skipping read '55' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 699s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 699s Warning: skipping read '86' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 699s Warning: skipping read '129' because length (1) <= # seed mismatches (0) 699s Warning: skipping read '129' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 699s 148 reads; of these: 699s 148 (100.00%) were unpaired; of these: 699s 129 (87.16%) aligned 0 times 699s 7 (4.73%) aligned exactly 1 time 699s 12 (8.11%) aligned >1 times 699s 12.84% overall alignment rate 699s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 699s Flattened IUPAC characters 699s Mutating sequence Sim.pm.2 699s Introducing 8 SNPs, 0/1 ref/read gaps, and 1 rearrangements 699s Finished SNPs 699s Finished ref gaps 699s Finished read gaps 699s Mutating sequence Sim.pm.1 699s Introducing 16 SNPs, 0/1 ref/read gaps, and 1 rearrangements 699s Finished SNPs 699s Finished ref gaps 699s Finished read gaps 699s Mutated reference genome to subject genome 699s SNPs introduced: 24 699s Reference gaps introduced: 0 699s Read gaps introduced: 2 699s Rearrangements introduced: 2 699s Created read sampler 699s Sampling 141 reads 699s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 699s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 699s parsing sequence Sim.pm.1... 699s parsing sequence Sim.pm.2... 699s Parsed 234 reference bases 699s *** Run 62 of 100 699s /usr/bin/bowtie2 --mm --rfg 32.9770277291757,1.33460815923367 --score-min L,7.16574540412443,8.30566786880688 --ma 9.26323739875815 --gbar 2 --cp-ival 1 -M 5 --large-index --cp-min 17 --trim5 6 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 699s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 699s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 699s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '1' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 699s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '5' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 699s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 699s Warning: skipping mate #2 of read '11' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 699s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '26' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 699s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '28' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 699s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '34' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 699s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '37' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 699s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '38' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 699s Warning: skipping mate #1 of read '45' because length (1) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '45' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 699s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '50' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 699s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '57' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 699s Read 50 alignments... 699s Read 100 alignments... 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 699s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '66' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 699s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '78' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 699s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '80' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 699s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '81' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 699s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '86' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 699s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '89' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 699s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 699s Warning: skipping read '92' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 699s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 699s Warning: skipping mate #2 of read '99' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 699s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '109' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 699s Read 150 alignments... 699s Read 200 alignments... 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 699s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '122' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 699s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '124' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 699s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '128' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 699s Warning: skipping mate #2 of read '129' because length (1) <= # seed mismatches (0) 699s Warning: skipping mate #2 of read '129' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 699s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '133' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 699s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 699s Warning: skipping read '135' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 699s 141 reads; of these: 699s 130 (92.20%) were paired; of these: 699s 126 (96.92%) aligned concordantly 0 times 699s 1 (0.77%) aligned concordantly exactly 1 time 699s 3 (2.31%) aligned concordantly >1 times 699s ---- 699s 126 pairs aligned concordantly 0 times; of these: 699s 0 (0.00%) aligned discordantly 1 time 699s ---- 699s 126 pairs aligned 0 times concordantly or discordantly; of these: 699s 252 mates make up the pairs; of these: 699s 217 (86.11%) aligned 0 times 699s 15 (5.95%) aligned exactly 1 time 699s 20 (7.94%) aligned >1 times 699s 11 (7.80%) were unpaired; of these: 699s 8 (72.73%) aligned 0 times 699s 2 (18.18%) aligned exactly 1 time 699s 1 (9.09%) aligned >1 times 699s 16.97% overall alignment rate 699s Read 250 alignments... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TCTCAGGTTGGAGTCCC 699s TCTCAGGTTGGAGTCCC 699s Processing line... 699s Processing line... 699s GAT 699s GAT 699s Processing line... 699s Processing line... 699s GGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCC 699s GGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GCCC 699s GCCC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GG 699s GG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CCGGTGTGTCGTTGTAGGCCGTTG 699s CCGGTGTGTCGTTGTAGGCCGTTG 699s Processing line... 699s GTTCCCGGTGTGTCGTTG 699s GTTCCCGGTGTGTCGTTG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CCGTTCCCGGTGTGTCGTTGTAGGCCGTTGG 699s CCGTTCCCGGTGTGTCGTTGTAGGCCGTTGG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GGTTTATGTCAT 699s GGTTTATGTCAT 699s Processing line... 699s GGT 699s GGT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TC 699s TC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TCGCGCGGTTGTTTGGT 699s TCGCGCGGTTGTTTGGT 699s Processing line... 699s Processing line... 699s TCGTTGTAGG 699s TCGTTGTAGG 699s Processing line... 699s Processing line... 699s TCGTTGTAGGCC 699s TCGTTGTAGGCC 699s Processing line... 699s Processing line... 699s CTGGTGACGCC 699s CTGGTGACGCC 699s Processing line... 699s GGTCTCAGGTTGGAGT 699s GGTCTCAGGTTGGAGT 699s Processing line... 699s GGTTGGTTTATGTCATCGCGCGGTTG 699s GGTTGGTTTATGTCATCGCGCGGTTG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GG 699s GG 699s Processing line... 699s TGCGG 699s TGCGG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTCATCGCGC 699s GTCATCGCGC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTG 699s GTG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CAGGTTGGAGTCCCGCGGC 699s CAGGTTGGAGTCCCGCGGC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TTAT 699s TTAT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTTCCCGGTGTGTC 699s GTTCCCGGTGTGTC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTGCGGCGGG 699s GTGCGGCGGG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTTGAAC 699s GTTGAAC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TGG 699s TGG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s AGTCC 699s AGTCC 699s Processing line... 699s Processing line... 699s Processing line... 699s GGTGC 699s GGTGC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTGTGTCGTTGTAGGCC 699s GTGTGTCGTTGTAGGCC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s ACGTGCG 699s ACGTGCG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GGTTGGTTTATGTCAT 699s GGTTGGTTTATGTCAT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CGCCGT 699s CGCCGT 699s Processing line... 699s Processing line... 699s GTTGTAGGCCGT 699s GTTGTAGGCCGT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TA 699s TA 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GGTGTGTCGT 699s GGTGTGTCGT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GCGTGGGTGCGGCGGGGCCAGTTCGATT 699s GCGTGGGTGCGGCGGGGCCAGTTCGATT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GGTTC 699s GGTTC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CCAGTTCGAT 699s CCAGTTCGAT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTCTCAG 699s GTCTCAG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CCCGCG 699s CCCGCG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTGTGTCGTTG 699s GTGTGTCGTTG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GGGTCTCAGG 699s GGGTCTCAGG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TTGGGGTTCGC 699s TTGGGGTTCGC 699s Processing line... 699s Processing line... 699s GTGGGTGCGGCGGGGCCAGTTCG 699s GTGGGTGCGGCGGGGCCAGTTCG 699s Processing line... 699s Processing line... 699s GTGTGTCGTTGTAGGC 699s GTGTGTCGTTGTAGGC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s --- Summary --- 699s Read 1 reference strings 699s Checked 46 alignments, 0 edits 699s --------------- 699s PASSED 699s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 699s /usr/bin/bowtie2 --mm --rfg 32.9770277291757,1.33460815923367 --score-min L,7.16574540412443,8.30566786880688 --ma 9.26323739875815 --gbar 2 --cp-ival 1 -M 5 --large-index --cp-min 17 --trim5 6 -r -p 3 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 699s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 699s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 699s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '1' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 699s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '5' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 699s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 699s Warning: skipping mate #2 of read '11' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 699s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '34' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 699s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '37' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 699s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '38' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 699s Warning: skipping mate #1 of read '45' because length (1) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '45' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 699s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '50' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 699s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '57' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 699s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '26' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 699s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '28' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 699s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '66' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 699s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '78' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 699s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '80' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 699s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '81' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 699s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '86' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 699s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '89' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 699s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 699s Warning: skipping read '92' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 699s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 699s Warning: skipping mate #2 of read '99' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 699s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '109' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 699s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '122' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 699s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '124' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 699s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '128' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 699s Warning: skipping mate #2 of read '129' because length (1) <= # seed mismatches (0) 699s Warning: skipping mate #2 of read '129' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 699s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '133' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 699s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 699s Warning: skipping read '135' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 699s 141 reads; of these: 699s 130 (92.20%) were paired; of these: 699s 126 (96.92%) aligned concordantly 0 times 699s 1 (0.77%) aligned concordantly exactly 1 time 699s 3 (2.31%) aligned concordantly >1 times 699s ---- 699s 126 pairs aligned concordantly 0 times; of these: 699s 0 (0.00%) aligned discordantly 1 time 699s ---- 699s 126 pairs aligned 0 times concordantly or discordantly; of these: 699s 252 mates make up the pairs; of these: 699s 217 (86.11%) aligned 0 times 699s 15 (5.95%) aligned exactly 1 time 699s 20 (7.94%) aligned >1 times 699s 11 (7.80%) were unpaired; of these: 699s 8 (72.73%) aligned 0 times 699s 2 (18.18%) aligned exactly 1 time 699s 1 (9.09%) aligned >1 times 699s 16.97% overall alignment rate 699s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 699s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 699s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 699s Flattened IUPAC characters 699s Mutating sequence Sim.pm.2 699s Introducing 6 SNPs, 0/2 ref/read gaps, and 0 rearrangements 699s Finished SNPs 699s Finished ref gaps 699s Finished read gaps 699s Mutating sequence Sim.pm.1 699s Introducing 1 SNPs, 0/3 ref/read gaps, and 4 rearrangements 699s Finished SNPs 699s Finished ref gaps 699s Finished read gaps 699s Mutated reference genome to subject genome 699s SNPs introduced: 7 699s Reference gaps introduced: 0 699s Read gaps introduced: 5 699s Rearrangements introduced: 4 699s Created read sampler 699s Sampling 101 reads 699s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 699s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 699s parsing sequence Sim.pm.1... 699s parsing sequence Sim.pm.2... 699s Parsed 234 reference bases 699s *** Run 63 of 100 699s /usr/bin/bowtie2 -D 24 --trim3 9 --ma 35.4610191873213 --score-min L,7.57448346765297,3.74417245167059 --rdg 12.2415146960545 --norc --trim5 0 --cp-min 8 -M 4 --large-index --cp-ival 2 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 699s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 699s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 699s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 699s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 699s Warning: skipping read '1' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 699s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 699s Warning: skipping read '20' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 699s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '29' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 699s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '39' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 699s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 699s Warning: skipping read '55' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 699s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '57' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 699s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '64' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 699s Read 50 alignments... 699s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 699s Read 100 alignments... 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 699s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '80' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 699s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '87' because it was < 2 characters long 699s Warning: skipping mate #2 of read '87' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 699s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '92' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 699s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 699s Warning: skipping mate #1 of read '99' because it was < 2 characters long 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 699s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 699s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 699s Warning: skipping read '101' because it was < 2 characters long 699s 101 reads; of these: 699s 84 (83.17%) were paired; of these: 699s 84 (100.00%) aligned concordantly 0 times 699s 0 (0.00%) aligned concordantly exactly 1 time 699s 0 (0.00%) aligned concordantly >1 times 699s ---- 699s 84 pairs aligned concordantly 0 times; of these: 699s 0 (0.00%) aligned discordantly 1 time 699s ---- 699s 84 pairs aligned 0 times concordantly or discordantly; of these: 699s 168 mates make up the pairs; of these: 699s 149 (88.69%) aligned 0 times 699s 5 (2.98%) aligned exactly 1 time 699s 14 (8.33%) aligned >1 times 699s 17 (16.83%) were unpaired; of these: 699s 14 (82.35%) aligned 0 times 699s 1 (5.88%) aligned exactly 1 time 699s 2 (11.76%) aligned >1 times 699s 11.89% overall alignment rate 699s Read 150 alignments... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TTGTAGGCCGTTGGGGTTC 699s TTGTAGGCCGTTGGGGTTC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTTGGTTTATGTCATCGCGC 699s GTTGGTTTATGTCATCGCGC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GGGTGCG 699s GGGTGCG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CGT 699s CGT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TGTG 699s TGTG 699s Processing line... 699s Processing line... 699s CCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGG 699s CCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GGTG 699s GGTG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GGGGCGTGGGTGCGGCGGGGCCAGTTCGATTC 699s GGGGCGTGGGTGCGGCGGGGCCAGTTCGATTC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CT 699s CT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTTTATGTCATCGCG 699s GTTTATGTCATCGCG 699s Processing line... 699s Processing line... 699s CCGGTGT 699s CCGGTGT 699s Processing line... 699s Processing line... 699s GGT 699s GGT 699s Processing line... 699s Processing line... 699s GGGGTT 699s GGGGTT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TGTGTCGTTGTAGGCCGTTGGGGTTCCC 699s TGTGTCGTTGTAGGCCGTTGGGGTTCCC 699s Processing line... 699s Processing line... 699s TTGTAGGCCG 699s TTGTAGGCCG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TTGGGGTT 699s TTGGGGTT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s GTGTCGTTGTAGGCCGTTGGGGT 699s GTGTCGTTGTAGGCCGTTGGGGT 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CCGGTGTGTCGTTGTAGGCCG 699s CCGGTGTGTCGTTGTAGGCCG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s CG 699s CG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s TTCGCC 699s TTCGCC 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s AGTCCCGCG 699s AGTCCCGCG 699s Processing line... 699s Processing line... 699s CCG 699s CCG 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s Processing line... 699s --- Summary --- 699s Read 1 reference strings 699s Checked 22 alignments, 0 edits 699s --------------- 699s PASSED 699s Flattened IUPAC characters 699s Mutating sequence Sim.pm.2 699s Introducing 2 SNPs, 2/2 ref/read gaps, and 0 rearrangements 699s Finished SNPs 699s Finished ref gaps 699s Finished read gaps 699s Mutating sequence Sim.pm.1 699s Introducing 9 SNPs, 2/1 ref/read gaps, and 1 rearrangements 699s Finished SNPs 699s Finished ref gaps 699s Finished read gaps 699s Mutated reference genome to subject genome 699s SNPs introduced: 11 699s Reference gaps introduced: 4 699s Read gaps introduced: 3 699s Rearrangements introduced: 1 699s Created read sampler 699s Sampling 80 reads 699s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 699s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 699s parsing sequence Sim.pm.1... 699s parsing sequence Sim.pm.2... 699s Parsed 234 reference bases 699s *** Run 64 of 100 699s /usr/bin/bowtie2 --local --cp-ival 1 -a --trim5 9 --rfg 45.7165873217908 --trim3 1 --mp 6.26263994366135,1.75180805376902 --large-index --np 1 --cp-min 4 --score-min L,7.30474461377752,5.41416416792383 -D 30 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 700s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 700s Warning: skipping read '3' because it was < 2 characters long 700s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '4' because it was < 2 characters long 700s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '9' because it was < 2 characters long 700s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read '25' because it was < 2 characters long 700s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '28' because it was < 2 characters long 700s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '30' because it was < 2 characters long 700s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '31' because it was < 2 characters long 700s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '36' because it was < 2 characters long 700s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '47' because it was < 2 characters long 700s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 700s Warning: skipping read '48' because it was < 2 characters long 700s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '49' because it was < 2 characters long 700s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '50' because it was < 2 characters long 700s Read 50 alignments... 700s Read 100 alignments... 700s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '67' because it was < 2 characters long 700s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 700s Warning: skipping read '74' because it was < 2 characters long 700s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '78' because it was < 2 characters long 700s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '79' because it was < 2 characters long 700s 80 reads; of these: 700s 68 (85.00%) were paired; of these: 700s 68 (100.00%) aligned concordantly 0 times 700s 0 (0.00%) aligned concordantly exactly 1 time 700s 0 (0.00%) aligned concordantly >1 times 700s ---- 700s 68 pairs aligned concordantly 0 times; of these: 700s 0 (0.00%) aligned discordantly 1 time 700s ---- 700s 68 pairs aligned 0 times concordantly or discordantly; of these: 700s 136 mates make up the pairs; of these: 700s 136 (100.00%) aligned 0 times 700s 0 (0.00%) aligned exactly 1 time 700s 0 (0.00%) aligned >1 times 700s 12 (15.00%) were unpaired; of these: 700s 12 (100.00%) aligned 0 times 700s 0 (0.00%) aligned exactly 1 time 700s 0 (0.00%) aligned >1 times 700s 0.00% overall alignment rate 700s Read 150 alignments... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s /usr/bin/bowtie2 --local --cp-ival 1 -a --trim5 9 --rfg 45.7165873217908 --trim3 1 --mp 6.26263994366135,1.75180805376902 --large-index --np 1 --cp-min 4 --score-min L,7.30474461377752,5.41416416792383 -D 30 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s --- Summary --- 700s Read 1 reference strings 700s Checked 0 alignments, 0 edits 700s --------------- 700s PASSED 700s ALSO checking that bowtie2 and bowtie2-align match up 700s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 700s Warning: skipping read '3' because it was < 2 characters long 700s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '4' because it was < 2 characters long 700s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '9' because it was < 2 characters long 700s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read '25' because it was < 2 characters long 700s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '28' because it was < 2 characters long 700s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '30' because it was < 2 characters long 700s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '31' because it was < 2 characters long 700s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '36' because it was < 2 characters long 700s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '47' because it was < 2 characters long 700s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 700s Warning: skipping read '48' because it was < 2 characters long 700s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '49' because it was < 2 characters long 700s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '50' because it was < 2 characters long 700s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '67' because it was < 2 characters long 700s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 700s Warning: skipping read '74' because it was < 2 characters long 700s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '78' because it was < 2 characters long 700s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read '79' because it was < 2 characters long 700s 80 reads; of these: 700s 68diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 700s (85.00%) were paired; of these: 700s 68 (100.00%) aligned concordantly 0 times 700s 0 (0.00%) aligned concordantly exactly 1 time 700s 0 (0.00%) aligned concordantly >1 times 700s ---- 700s 68 pairs aligned concordantly 0 times; of these: 700s 0 (0.00%) aligned discordantly 1 time 700s ---- 700s 68 pairs aligned 0 times concordantly or discordantly; of these: 700s 136 mates make up the pairs; of these: 700s 136 (100.00%) aligned 0 times 700s 0 (0.00%) aligned exactly 1 time 700s 0 (0.00%) aligned >1 times 700s 12 (15.00%) were unpaired; of these: 700s 12 (100.00%) aligned 0 times 700s 0 (0.00%) aligned exactly 1 time 700s 0 (0.00%) aligned >1 times 700s 0.00% overall alignment rate 700s Flattened IUPAC characters 700s Mutating sequence Sim.pm.1 700s Introducing 7 SNPs, 0/4 ref/read gaps, and 0 rearrangements 700s Finished SNPs 700s Finished ref gaps 700s Finished read gaps 700s Mutating sequence Sim.pm.2 700s Introducing 15 SNPs, 2/1 ref/read gaps, and 0 rearrangements 700s Finished SNPs 700s Finished ref gaps 700s Finished read gaps 700s Mutated reference genome to subject genome 700s SNPs introduced: 22 700s Reference gaps introduced: 2 700s Read gaps introduced: 5 700s Rearrangements introduced: 0 700s Created read sampler 700s Sampling 71 reads 700s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 700s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 700s parsing sequence Sim.pm.1... 700s parsing sequence Sim.pm.2... 700s Parsed 234 reference bases 700s *** Run 65 of 100 700s /usr/bin/bowtie2 --ma 29.8928396566265 --score-min L,7.68983703415662,6.87819586444956 --rfg 34.9399968548211 --trim5 8 --n-ceil 0.568868019084345,0.744198361764132 --np 2 --cp-min 3 --large-index --cp-ival 1 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq 700s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 700s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 700s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 700s Read 50 alignments... 700s Read 100 alignments... 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 700s 71 reads; of these: 700s 60 (84.51%) were paired; of these: 700s 60 (100.00%) aligned concordantly 0 times 700s 0 (0.00%) aligned concordantly exactly 1 time 700s 0 (0.00%) aligned concordantly >1 times 700s ---- 700s 60 pairs aligned concordantly 0 times; of these: 700s 0 (0.00%) aligned discordantly 1 time 700s ---- 700s 60 pairs aligned 0 times concordantly or discordantly; of these: 700s 120 mates make up the pairs; of these: 700s 99 (82.50%) aligned 0 times 700s 11 (9.17%) aligned exactly 1 time 700s 10 (8.33%) aligned >1 times 700s 11 (15.49%) were unpaired; of these: 700s 9 (81.82%) aligned 0 times 700s 2 (18.18%) aligned exactly 1 time 700s 0 (0.00%) aligned >1 times 700s 17.56% overall alignment rate 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s AGT 700s AGT 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s TGGAGTCCCGC 700s TGGAGTCCCGC 700s Processing line... 700s Processing line... 700s GGGTTCGCCGTTCCCGGT 700s GGGTTCGCCGTTCCCGGT 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s TATG 700s TATG 700s Processing line... 700s Processing line... 700s /usr/bin/bowtie2 --ma 29.8928396566265 --score-min L,7.68983703415662,6.87819586444956 --rfg 34.9399968548211 --trim5 8 --n-ceil 0.568868019084345,0.744198361764132 --np 2 --cp-min 3 --large-index --cp-ival 1 --qseq -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 700s CC 700s CC 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s TCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTC 700s TCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTC 700s Processing line... 700s Processing line... 700s GGG 700s GGG 700s Processing line... 700s Processing line... 700s GCCGT 700s GCCGT 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s ACGTG 700s ACGTG 700s Processing line... 700s Processing line... 700s Processing line... 700s GGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCC 700s GGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCC 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s TGG 700s TGG 700s Processing line... 700s Processing line... 700s Processing line... 700s GGTCTCAGGTTGG 700s GGTCTCAGGTTGG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGT 700s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGT 700s Processing line... 700s TCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTG 700s TCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTG 700s Processing line... 700s Processing line... 700s GGTGACGCCG 700s GGTGACGCCG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s GCG 700s GCG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s GCCAGTTCGATTC 700s GCCAGTTCGATTC 700s Processing line... 700s Processing line... 700s AGGCCGTTGGGGTTCGCC 700s AGGCCGTTGGGGTTCGCC 700s Processing line... 700s Processing line... 700s GATTC 700s GATTC 700s Processing line... 700s Processing line... 700s GTCTCAGGTTGGAGTCCCGCGGCCCGTT 700s GTCTCAGGTTGGAGTCCCGCGGCCCGTT 700s Processing line... 700s Processing line... 700s GTTC 700s GTTC 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s CG 700s CG 700s Processing line... 700s Processing line... 700s Processing line... 700s TTCGCCGTTCCCGGTGTGTCGTTGTAGGC 700s TTCGCCGTTCCCGGTGTGTCGTTGTAGGC 700s Processing line... 700s --- Summary --- 700s Read 1 reference strings 700s Checked 23 alignments, 0 edits 700s --------------- 700s PASSED 700s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 700s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 700s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 700s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 700s 71 reads; of these: 700s 60 (84.51%) were paired; of these: 700s 60 (100.00%) aligned concordantly 0 times 700s 0 (0.00%) aligned concordantly exactly 1 time 700s 0 (0.00%) aligned concordantly >1 times 700s ---- 700s 60 pairs aligned concordantly 0 times; of these: 700s 0 (0.00%) aligned discordantly 1 time 700s ---- 700s 60 pairs aligned 0 times concordantly or discordantly; of these: 700s 120 mates make up the pairs; of these: 700s 99 (82.50%) aligned 0 times 700s 11 (9.17%) aligned exactly 1 time 700s 10 (8.33%) aligned >1 times 700s 11 (15.49%) were unpaired; of these: 700s 9 (81.82%) aligned 0 times 700s 2 (18.18%) aligned exactly 1 time 700s 0 (0.00%) aligned >1 times 700s 17.56% overall alignment rate 700s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 700s Flattened IUPAC characters 700s Mutating sequence Sim.pm.2 700s Introducing 8 SNPs, 0/1 ref/read gaps, and 1 rearrangements 700s Finished SNPs 700s Finished ref gaps 700s Finished read gaps 700s Mutating sequence Sim.pm.1 700s Introducing 2 SNPs, 1/0 ref/read gaps, and 1 rearrangements 700s Finished SNPs 700s Finished ref gaps 700s Finished read gaps 700s Mutated reference genome to subject genome 700s SNPs introduced: 10 700s Reference gaps introduced: 1 700s Read gaps introduced: 1 700s Rearrangements introduced: 2 700s Created read sampler 700s Sampling 100 reads 700s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 700s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 700s parsing sequence Sim.pm.1... 700s parsing sequence Sim.pm.2... 700s Parsed 234 reference bases 700s *** Run 66 of 100 700s /usr/bin/bowtie2 --large-index --cp-min 3 --np 6 --cp-ival 1 -D 27 -i L,2.4803000571325 --score-min L,7.06109474468653,7.19236461974261 --ma 39.6404807378728 --nofw --mm --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq 700s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 700s Read 50 alignments... 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 700s Read 100 alignments... 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 700s Read 150 alignments... 700s 100 reads; of these: 700s 100 (100.00%) were paired; of these: 700s 99 (99.00%) aligned concordantly 0 times 700s 0 (0.00%) aligned concordantly exactly 1 time 700s 1 (1.00%) aligned concordantly >1 times 700s ---- 700s 99 pairs aligned concordantly 0 times; of these: 700s 0 (0.00%) aligned discordantly 1 time 700s ---- 700s 99 pairs aligned 0 times concordantly or discordantly; of these: 700s 198 mates make up the pairs; of these: 700s 170 (85.86%) aligned 0 times 700s 10 (5.05%) aligned exactly 1 time 700s 18 (9.09%) aligned >1 times 700s 15.00% overall alignment rate 700s Read 200 alignments... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s CCC 700s CCC 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s GTTGTAGGCCGTTGGGGTTCGCCGTTC 700s GTTGTAGGCCGTTGGGGTTCGCCGTTC 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s TGTTTG 700s TGTTTG 700s Processing line... 700s Processing line... 700s CCGTTCCCGGTGTG 700s CCGTTCCCGGTGTG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s TGTGTCGTTGTAGGCC 700s TGTGTCGTTGTAGGCC 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s CGCCGTTCCC 700s CGCCGTTCCC 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s ACGCC 700s ACGCC 700s Processing line... 700s Processing line... 700s GTGG 700s GTGG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s CGGTGTGTCGTTGTAGGCCGTTGG 700s CGGTGTGTCGTTGTAGGCCGTTGG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s GTGGG 700s GTGGG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s GTGCGGCGGGGCCAGTT 700s GTGCGGCGGGGCCAGTT 700s Processing line... 700s Processing line... 700s CCGTTCCCGG 700s CCGTTCCCGG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s CCCG 700s CCCG 700s Processing line... 700s Processing line... 700s TGTCGTTGTAGGCCGTTGGGG 700s TGTCGTTGTAGGCCGTTGGGG 700s Processing line... 700s Processing line... 700s AG 700s AG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s ACGTGCGGCG 700s ACGTGCGGCG 700s Processing line... 700s Processing line... 700s CG 700s CG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s CCGTTGGGGTTCGCCGTTCCCGGTGTGTCG 700s CCGTTGGGGTTCGCCGTTCCCGGTGTGTCG 700s Processing line... 700s CGGTGTG 700s CGGTGTG 700s Processing line... 700s GGGTTCGCCGTTC 700s GGGTTCGCCGTTC 700s Processing line... 700s Processing line... 700s GCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 700s GCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s GCG 700s GCG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s TGTAGGCCGTTG 700s TGTAGGCCGTTG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s CGGCGGGGCCAGTTCGATTC 700s CGGCGGGGCCAGTTCGATTC 700s Processing line... 700s Processing line... 700s GGCCG 700s GGCCG 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s GTGCGGCGGGGCCAGTTCGATTCGGTTG 700s GTGCGGCGGGGCCAGTTCGATTCGGTTG 700s Processing line... 700s Processing line... 700s GTGTGTCGTTGT 700s GTGTGTCGTTGT 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s GA 700s GA 700s Processing line... 700s GGGGTTCGCC 700s GGGGTTCGCC 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s CGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGT 700s CGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGT 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s --- Summary --- 700s Read 1 reference strings 700s Checked 30 alignments, 0 edits 700s --------------- 700s PASSED 700s ALSO checking that bowtie2 and bowtie2-align match up 700s /usr/bin/bowtie2 --large-index --cp-min 3 --np 6 --cp-ival 1 -D 27 -i L,2.4803000571325 --score-min L,7.06109474468653,7.19236461974261 --ma 39.6404807378728 --nofw --mm --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 700s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 700s 100 reads; of these: 700s 100 (100.00%) were paired; of these: 700s 99 (99.00%) aligned concordantly 0 times 700s 0 (0.00%) aligned concordantly exactly 1 time 700s 1 (1.00%) aligned concordantly >1 times 700s ---- 700s 99 pairs aligned concordantly 0 times; of these: 700s 0 (0.00%) aligned discordantly 1 time 700s ---- 700s 99 pairs aligned 0 times concordantly or discordantly; of these: 700s 198 mates make up the pairs; of these: 700s 170 (85.86%) aligned 0 times 700s 10 (5.05%) aligned exactly 1 time 700s 18 (9.09%) aligned >1 times 700s 15.00% overall alignment rate 700s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 700s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 700s /usr/bin/bowtie2 --large-index --cp-min 3 --np 6 --cp-ival 1 -D 27 -i L,2.4803000571325 --score-min L,7.06109474468653,7.19236461974261 --ma 39.6404807378728 --nofw --mm --qseq -p 2 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 700s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 700s 100 reads; of these: 700s 100 (100.00%) were paired; of these: 700s 99 (99.00%) aligned concordantly 0 times 700s 0 (0.00%) aligned concordantly exactly 1 time 700s 1 (1.00%) aligned concordantly >1 times 700s ---- 700s 99 pairs aligned concordantly 0 times; of these: 700s 0 (0.00%) aligned discordantly 1 time 700s ---- 700s 99 pairs aligned 0 times concordantly or discordantly; of these: 700s 198 mates make up the pairs; of these: 700s 170 (85.86%) aligned 0 times 700s 10 (5.05%) aligned exactly 1 time 700s 18 (9.09%) aligned >1 times 700s 15.00% overall alignment rate 700s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 700s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 700s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 700s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 700s /usr/bin/bowtie2 --large-index --cp-min 3 --np 6 --cp-ival 1 -D 27 -i L,2.4803000571325 --score-min L,7.06109474468653,7.19236461974261 --ma 39.6404807378728 --nofw --mm --qseq -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 700s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 700s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 700s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (0) 700s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 700s 100 reads; of these: 700s 100 (100.00%) were paired; of these: 700s 99 (99.00%) aligned concordantly 0 times 700s 0 (0.00%) aligned concordantly exactly 1 time 700s 1 (1.00%) aligned concordantly >1 times 700s ---- 700s 99 pairs aligned concordantly 0 times; of these: 700s 0 (0.00%) aligned discordantly 1 time 700s ---- 700s 99 pairs aligned 0 times concordantly or discordantly; of these: 700s 198 mates make up the pairs; of these: 700s 170 (85.86%) aligned 0 times 700s 10 (5.05%) aligned exactly 1 time 700s 18 (9.09%) aligned >1 times 700s 15.00% overall alignment rate 700s Flattened IUPAC characters 700s Mutating sequence Sim.pm.1 700s Introducing 8 SNPs, 2/0 ref/read gaps, and 2 rearrangements 700s Finished SNPs 700s Finished ref gaps 700s Finished read gaps 700s Mutating sequence Sim.pm.2 700s Introducing 22 SNPs, 0/1 ref/read gaps, and 2 rearrangements 700s Finished SNPs 700s Finished ref gaps 700s Finished read gaps 700s Mutated reference genome to subject genome 700s SNPs introduced: 30 700s Reference gaps introduced: 2 700s Read gaps introduced: 1 700s Rearrangements introduced: 4 700s Created read sampler 700s Sampling 54 reads 700s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 700s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 700s parsing sequence Sim.pm.1... 700s parsing sequence Sim.pm.2... 700s Parsed 234 reference bases 700s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 700s *** Run 67 of 100 700s /usr/bin/bowtie2 --mp 9.83546861122122,4.55067020459425 --nofw --trim3 1 --cp-ival 1 --norc --rdg 40.2916763498413,13.167557905541 --score-min L,3.58074731489808,5.60102635579521 --large-index --np 1 --cp-min 10 -f -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta 700s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 700s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 700s Warning: skipping read '36' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 700s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 700s Warning: skipping read '41' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 700s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 700s Warning: skipping read '50' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 700s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 700s Warning: skipping read '53' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 700s 54 reads; of these: 700s 54 (100.00%) were unpaired; of these: 700s 54 (100.00%) aligned 0 times 700s 0 (0.00%) aligned exactly 1 time 700s 0 (0.00%) aligned >1 times 700s 0.00% overall alignment rate 700s Read 50 alignments... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s Processing line... 700s --- Summary --- 700s Read 1 reference strings 700s Checked 0 alignments, 0 edits 700s --------------- 700s PASSED 700s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 700s /usr/bin/bowtie2 --mp 9.83546861122122,4.55067020459425 --nofw --trim3 1 --cp-ival 1 --norc --rdg 40.2916763498413,13.167557905541 --score-min L,3.58074731489808,5.60102635579521 --large-index --np 1 --cp-min 10 -f -p 4 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 700s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 700s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 700s Warning: skipping read '36' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 700s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 700s Warning: skipping read '41' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 700s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 700s Warning: skipping read '50' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 700s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 700s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 700s Warning: skipping read '53' because it was < 2 characters long 700s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 701s 54 reads; of these: 701s 54 (100.00%) were unpaired; of these: 701s 54 (100.00%) aligned 0 times 701s 0 (0.00%) aligned exactly 1 time 701s 0 (0.00%) aligned >1 times 701s 0.00% overall alignment rate 701s Flattened IUPAC characters 701s Mutating sequence Sim.pm.1 701s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 701s Introducing 3 SNPs, 1/2 ref/read gaps, and 0 rearrangements 701s Finished SNPs 701s Finished ref gaps 701s Finished read gaps 701s Mutating sequence Sim.pm.2 701s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 701s Finished SNPs 701s Finished ref gaps 701s Finished read gaps 701s Mutated reference genome to subject genome 701s SNPs introduced: 6 701s Reference gaps introduced: 1 701s Read gaps introduced: 3 701s Rearrangements introduced: 0 701s Created read sampler 701s Sampling 65 reads 701s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 701s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 701s parsing sequence Sim.pm.1... 701s parsing sequence Sim.pm.2... 701s Parsed 234 reference bases 701s *** Run 68 of 100 701s /usr/bin/bowtie2 --large-index --cp-min 5 --np 1 --cp-ival 1 --score-min L,1.12325760930632,4.86152003623043 --ma 29.2055821714338 -k 3 -N 1 -L29 -i C,3.20142811030214,12.2415104352536 --mm --rfg 27.2818661923328,8.9984207143382 -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta 701s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 701s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #2 of read '17' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 701s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #2 of read '47' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 701s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #1 of read '49' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 701s Read 50 alignments... 701s Read 100 alignments... 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 701s 65 reads; of these: 701s 65 (100.00%) were paired; of these: 701s 63 (96.92%) aligned concordantly 0 times 701s 0 (0.00%) aligned concordantly exactly 1 time 701s 2 (3.08%) aligned concordantly >1 times 701s ---- 701s 63 pairs aligned concordantly 0 times; of these: 701s 1 (1.59%) aligned discordantly 1 time 701s ---- 701s 62 pairs aligned 0 times concordantly or discordantly; of these: 701s 124 mates make up the pairs; of these: 701s 99 (79.84%) aligned 0 times 701s 10 (8.06%) aligned exactly 1 time 701s 15 (12.10%) aligned >1 times 701s 23.85% overall alignment rate 701s Read 150 alignments... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s CG 701s CG 701s Processing line... 701s CCGTTC 701s CCGTTC 701s Processing line... 701s CG 701s CG 701s Processing line... 701s CCGTTC 701s CCGTTC 701s Processing line... 701s CG 701s CG 701s Processing line... 701s CCGTTC 701s CCGTTC 701s Processing line... 701s Processing line... 701s Processing line... 701s GGGCCAG 701s GGGCCAG 701s Processing line... 701s GGGCCAG 701s GGGCCAG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s CGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 701s CGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 701s Processing line... 701s CGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 701s CGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 701s Processing line... 701s Processing line... 701s TTGTAGGCCGTTGGG 701s TTGTAGGCCGTTGGG 701s Processing line... 701s TTGTAGGCCGTTGGG 701s TTGTAGGCCGTTGGG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GGCCAGTTCGATTCGGTTGGTTTATGTCATCGC 701s GGCCAGTTCGATTCGGTTGGTTTATGTCATCGC 701s Processing line... 701s GCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGT 701s GCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGT 701s Processing line... 701s TTCGCC 701s TTCGCC 701s Processing line... 701s TTCGCC 701s TTCGCC 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GTA 701s GTA 701s Processing line... 701s GTA 701s GTA 701s Processing line... 701s GTA 701s GTA 701s Processing line... 701s Processing line... 701s GTAGG 701s GTAGG 701s Processing line... 701s GTAGG 701s GTAGG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s CCGGTG 701s CCGGTG 701s Processing line... 701s CCGGTG 701s CCGGTG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GGCGGGGCCAGTTCGAT 701s GGCGGGGCCAGTTCGAT 701s Processing line... 701s Processing line... 701s GCGGTTGTTTGGTGTG 701s GCGGTTGTTTGGTGTG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s CGTTCCCGGTGTGTCGT 701s CGTTCCCGGTGTGTCGT 701s Processing line... 701s CGTTCCCGGTGTGTCGT 701s CGTTCCCGGTGTGTCGT 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s CCGTTGGGGT 701s CCGTTGGGGT 701s Processing line... 701s CCGTTGGGGT 701s CCGTTGGGGT 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s ACGCCGTTGAACGTGCGGCGGGGCC 701s ACGCCGTTGAACGTGCGGCGGGGCC 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s ACGCCGTTGAACGTGC 701s ACGCCGTTGAACGTGC 701s Processing line... 701s Processing line... 701s CTCAGGTTGGAGTCCCGCG 701s CTCAGGTTGGAGTCCCGCG 701s Processing line... 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s TTCGGT 701s TTCGGT 701s Processing line... 701s Processing line... 701s GCGGGGCC 701s GCGGGGCC 701s Processing line... 701s GCGGGGCC 701s GCGGGGCC 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GTAGGCCGTTGGGGTTCCCT 701s GTAGGCCGTTGGGGTTCCCT 701s Processing line... 701s Processing line... 701s GACGCCGTTGAA 701s GACGCCGTTGAA 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GGGGTTCGCCGTTCCC 701s GGGGTTCGCCGTTCCC 701s Processing line... 701s GGGGTTCGCCGTTCCC 701s GGGGTTCGCCGTTCCC 701s Processing line... 701s Processing line... 701s ATTCGGTTGGT 701s ATTCGGTTGGT 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s TCGGTTGGTTT 701s TCGGTTGGTTT 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GCG 701s GCG 701s Processing line... 701s AGTTCGATTCGGTTGGTTTATGTCATCGCGCG 701s AGTTCGATTCGGTTGGTTTATGTCATCGCGCG 701s Processing line... 701s GCG 701s GCG 701s Processing line... 701s AGTTCGATTCGGTTGGTTTATGTCATCGCGCG 701s AGTTCGATTCGGTTGGTTTATGTCATCGCGCG 701s Processing line... 701s GCG 701s GCG 701s Processing line... 701s AGTTCGATTCGGTTGGTTTATGTCATCGCGCG 701s AGTTCGATTCGGTTGGTTTATGTCATCGCGCG 701s Processing line... 701s Processing line... 701s Processing line... 701s GTTGGGGTTCGCCGTTCCCGGTG 701s GTTGGGGTTCGCCGTTCCCGGTG 701s Processing line... 701s GTTGGGGTTCGCCGTTCCCGGTG 701s GTTGGGGTTCGCCGTTCCCGGTG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s CGCCGTTCCCGGTGTGTCGTTGTAG 701s CGCCGTTCCCGGTGTGTCGTTGTAG 701s Processing line... 701s CGCCGTTCCCGGTGTGTCGTTGTAG 701s CGCCGTTCCCGGTGTGTCGTTGTAG 701s Processing line... 701s Processing line... 701s TCGTTGTAG 701s TCGTTGTAG 701s Processing line... 701s TCGTTGTAG 701s TCGTTGTAG 701s Processing line... 701s --- Summary --- 701s Read 1 reference strings 701s Checked 56 alignments, 0 edits 701s --------------- 701s PASSED 701s ALSO checking that bowtie2 and bowtie2-align match up 701s /usr/bin/bowtie2 --large-index --cp-min 5 --np 1 --cp-ival 1 --score-min L,1.12325760930632,4.86152003623043 --ma 29.2055821714338 -k 3 -N 1 -L29 -i C,3.20142811030214,12.2415104352536 --mm --rfg 27.2818661923328,8.9984207143382 -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 701s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 701s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #2 of read '17' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 701s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #2 of read '47' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 701s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #1 of read '49' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 701s 65 reads; of these: 701s 65 (100.00%) were paired; of these: 701s 63 (96.92%) aligned concordantly 0 times 701s 0 (0.00%) aligned concordantly exactly 1 time 701s 2 (3.08%) aligned concordantly >1 times 701s ---- 701s 63 pairs aligned concordantly 0 times; of these: 701s 1 (1.59%) aligned discordantly 1 time 701s ---- 701s 62 pairs aligned 0 times concordantly or discordantly; of these: 701s 124 mates make up the pairs; of these: 701s 99 (79.84%) aligned 0 times 701s 10 (8.06%) aligned exactly 1 time 701s 15 (12.10%) aligned >1 times 701s 23.85% overall alignment rate 701s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 701s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 701s /usr/bin/bowtie2 --large-index --cp-min 5 --np 1 --cp-ival 1 --score-min L,1.12325760930632,4.86152003623043 --ma 29.2055821714338 -k 3 -N 1 -L29 -i C,3.20142811030214,12.2415104352536 --mm --rfg 27.2818661923328,8.9984207143382 -f -p 2 -x /tmp/Sim.pm.RKKEKvBt --reorder -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 701s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 701s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #2 of read '17' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 701s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #1 of read '49' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 701s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #2 of read '47' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 701s 65 reads; of these: 701s 65 (100.00%) were paired; of these: 701s 63 (96.92%) aligned concordantly 0 times 701s 0 (0.00%) aligned concordantly exactly 1 time 701s 2 (3.08%) aligned concordantly >1 times 701s ---- 701s 63 pairs aligned concordantly 0 times; of these: 701s 1 (1.59%) aligned discordantly 1 time 701s ---- 701s 62 pairs aligned 0 times concordantly or discordantly; of these: 701s 124 mates make up the pairs; of these: 701s 99 (79.84%) aligned 0 times 701s 10 (8.06%) aligned exactly 1 time 701s 15 (12.10%) aligned >1 times 701s 23.85% overall alignment rate 701s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 701s Flattened IUPAC characters 701s Mutating sequence Sim.pm.1 701s Introducing 10 SNPs, 0/0 ref/read gaps, and 3 rearrangements 701s Finished SNPs 701s Finished ref gaps 701s Finished read gaps 701s Mutating sequence Sim.pm.2 701s Introducing 11 SNPs, 1/0 ref/read gaps, and 0 rearrangements 701s Finished SNPs 701s Finished ref gaps 701s Finished read gaps 701s Mutated reference genome to subject genome 701s SNPs introduced: 21 701s Reference gaps introduced: 1 701s Read gaps introduced: 0 701s Rearrangements introduced: 3 701s Created read sampler 701s Sampling 121 reads 701s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 701s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 701s parsing sequence Sim.pm.1... 701s parsing sequence Sim.pm.2... 701s Parsed 234 reference bases 701s *** Run 69 of 100 701s /usr/bin/bowtie2 --large-index --cp-min 2 --rdg 42.6889872185718,16.4275607081794 --score-min L,3.29266774136422,6.39942648585478 --local --cp-ival 1 -M 6 --n-ceil 1.49180124318372,1.03864116840274 --norc --trim3 0 -i S,2.60331868998804 -N 1 -L24 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 701s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 701s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #1 of read '7' because it was < 2 characters long 701s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #1 of read '12' because it was < 2 characters long 701s Warning: skipping mate #1 of read '68' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #1 of read '68' because it was < 2 characters long 701s Read 50 alignments... 701s Read 100 alignments... 701s Warning: skipping mate #2 of read '88' because length (1) <= # seed mismatches (1) 701s Warning: skipping mate #2 of read '88' because it was < 2 characters long 701s 121 reads; of these: 701s 121 (100.00%) were paired; of these: 701s 121 (100.00%) aligned concordantly 0 times 701s 0 (0.00%) aligned concordantly exactly 1 time 701s 0 (0.00%) aligned concordantly >1 times 701s ---- 701s 121 pairs aligned concordantly 0 times; of these: 701s 0 (0.00%) aligned discordantly 1 time 701s ---- 701s 121 pairs aligned 0 times concordantly or discordantly; of these: 701s 242 mates make up the pairs; of these: 701s 242 (100.00%) aligned 0 times 701s 0 (0.00%) aligned exactly 1 time 701s 0 (0.00%) aligned >1 times 701s 0.00% overall alignment rate 701s Read 150 alignments... 701s Read 200 alignments... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s --- Summary --- 701s Read 1 reference strings 701s Checked 0 alignments, 0 edits 701s --------------- 701s PASSED 701s *** Run 70 of 100 701s /usr/bin/bowtie2 --large-index --np 2 --cp-min 8 --rdg 20.256782863674,13.9494807951645 --mm --score-min L,5.80501231990105,2.07464973644597 --gbar 5 --cp-ival 1 -a --trim5 8 --n-ceil 0.324865996192028,0.263966345897475 --rfg 21.4811076265267,3.54574081552586 --trim3 2 --nofw --mp 9.16809473200145,7.74038969396294 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 701s Flattened IUPAC characters 701s Mutating sequence Sim.pm.1 701s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 701s Finished SNPs 701s Finished ref gaps 701s Finished read gaps 701s Mutating sequence Sim.pm.2 701s Introducing 13 SNPs, 0/1 ref/read gaps, and 1 rearrangements 701s Finished SNPs 701s Finished ref gaps 701s Finished read gaps 701s Mutated reference genome to subject genome 701s SNPs introduced: 13 701s Reference gaps introduced: 1 701s Read gaps introduced: 1 701s Rearrangements introduced: 2 701s Created read sampler 701s Sampling 159 reads 701s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 701s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 701s parsing sequence Sim.pm.1... 701s parsing sequence Sim.pm.2... 701s Parsed 234 reference bases 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 701s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '3' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 701s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '7' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 701s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '9' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 701s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '14' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 701s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '31' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 701s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '33' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 701s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '34' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 701s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '37' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 701s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '44' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 701s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '45' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 701s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '46' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 701s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '85' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 701s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '89' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 701s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 701s Warning: skipping read '92' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 701s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '97' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 701s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '101' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 701s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '105' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 701s Read 50 alignments... 701s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 701s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 701s Warning: skipping read '113' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 701s Warning: skipping mate #1 of read '121' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '121' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 701s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '124' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 701s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '128' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 701s Warning: skipping mate #1 of read '142' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '142' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 701s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '143' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 701s Warning: skipping mate #1 of read '147' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '147' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 701s Warning: skipping mate #1 of read '148' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '148' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 701s Warning: skipping mate #1 of read '156' because length (0) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '156' because it was < 2 characters long 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 701s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 701s 159 reads; of these: 701s 128 (80.50%) were paired; of these: 701s 127 (99.22%) aligned concordantly 0 times 701s 0 (0.00%) aligned concordantly exactly 1 time 701s 1 (0.78%) aligned concordantly >1 times 701s ---- 701s 127 pairs aligned concordantly 0 times; of these: 701s 0 (0.00%) aligned discordantly 1 time 701s ---- 701s 127 pairs aligned 0 times concordantly or discordantly; of these: 701s 254 mates make up the pairs; of these: 701s 234 (92.13%) aligned 0 times 701s 12 (4.72%) aligned exactly 1 time 701s 8 (3.15%) aligned >1 times 701s 31 (19.50%) were unpaired; of these: 701s 28 (90.32%) aligned 0 times 701s 0 (0.00%) aligned exactly 1 time 701s 3 (9.68%) aligned >1 times 701s 8.71% overall alignment rate 701s Read 100 alignments... 701s Read 150 alignments... 701s Read 200 alignments... 701s Read 250 alignments... 701s Read 300 alignments... 701s Read 350 alignments... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s TCC 701s TCC 701s Processing line... 701s TCC 701s TCC 701s Processing line... 701s TCC 701s TCC 701s Processing line... 701s TCC 701s TCC 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GGTTCGCCG 701s GGTTCGCCG 701s Processing line... 701s GGTTCGCCG 701s GGTTCGCCG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GGGGGCGTGGGT 701s GGGGGCGTGGGT 701s Processing line... 701s Processing line... 701s Processing line... 701s TTGTAGGC 701s TTGTAGGC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s TTGTAGGC 701s TTGTAGGC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s TTGTAGGC 701s TTGTAGGC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s TTGTAGGC 701s TTGTAGGC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s TTGTAGGC 701s TTGTAGGC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s TTGTAGGC 701s TTGTAGGC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s TTGTAGGC 701s TTGTAGGC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s TTGTAGGC 701s TTGTAGGC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s TTGTAGGC 701s TTGTAGGC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s TTGTAGGC 701s TTGTAGGC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s CCGTTCCCGGTGTGTCG 701s CCGTTCCCGGTGTGTCG 701s Processing line... 701s CCGTTCCCGGTGTGTCG 701s CCGTTCCCGGTGTGTCG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s CCAGTTCGATTCGG 701s CCAGTTCGATTCGG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s TGAACGTGC 701s TGAACGTGC 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s CCGGTGTGTCG 701s CCGGTGTGTCG 701s Processing line... 701s CCGGTGTGTCG 701s CCGGTGTGTCG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s TTG 701s TTG 701s Processing line... 701s TTG 701s TTG 701s Processing line... 701s TTG 701s TTG 701s Processing line... 701s TTG 701s TTG 701s Processing line... 701s TTG 701s TTG 701s Processing line... 701s TTG 701s TTG 701s Processing line... 701s TTG 701s TTG 701s Processing line... 701s TTG 701s TTG 701s Processing line... 701s TTG 701s TTG 701s Processing line... 701s TTG 701s TTG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GGCCGTTGGGGTTCGCCGT 701s GGCCGTTGGGGTTCGCCGT 701s Processing line... 701s Processing line... 701s GGGGTT 701s GGGGTT 701s Processing line... 701s GGGGTT 701s GGGGTT 701s Processing line... 701s GGGGTT 701s GGGGTT 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GGTCTCAGGTTGGAGTCC 701s GGTCTCAGGTTGGAGTCC 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s AG 701s AG 701s Processing line... 701s AG 701s AG 701s Processing line... 701s AG 701s AG 701s Processing line... 701s AG 701s AG 701s Processing line... 701s AG 701s AG 701s Processing line... 701s AG 701s AG 701s Processing line... 701s AG 701s AG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s CGTGGGTGC 701s CGTGGGTGC 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GTTGTAGGCCGTTGGGGTTCGCCGTTC 701s GTTGTAGGCCGTTGGGGTTCGCCGTTC 701s Processing line... 701s Processing line... 701s CGGGGGTCTCAGGTTG 701s CGGGGGTCTCAGGTTG 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GACG 701s GACG 701s Processing line... 701s TTCGCCGTTCCC 701s TTCGCCGTTCCC 701s Processing line... 701s TTCGCCGTTCCC 701s TTCGCCGTTCCC 701s Processing line... 701s Processing line... 701s Processing line... 701s CCGGTGTGT 701s CCGGTGTGT 701s Processing line... 701s CCGGTGTGT 701s CCGGTGTGT 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s TCCCGGTGTGTCGTTGTAGGCCGTTGGG 701s TCCCGGTGTGTCGTTGTAGGCCGTTGGG 701s Processing line... 701s TCCCGGTGTGTCGTTGTAGGCCGTTGGG 701s TCCCGGTGTGTCGTTGTAGGCCGTTGGG 701s Processing line... 701s Processing line... 701s GGGTCTCAGGTT 701s GGGTCTCAGGTT 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s CC 701s CC 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s GGGGGTCTCAGGTTGGAGTCCCGC 701s GGGGGTCTCAGGTTGGAGTCCCGC 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s CTGG 701s CTGG 701s Processing line... 701s --- Summary --- 701s Read 1 reference strings 701s Checked 85 alignments, 0 edits 701s --------------- 701s PASSED 701s Flattened IUPAC characters 701s Mutating sequence Sim.pm.1 701s Introducing 23 SNPs, 1/0 ref/read gaps, and 0 rearrangements 701s Finished SNPs 701s Finished ref gaps 701s Finished read gaps 701s Mutating sequence Sim.pm.2 701s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 701s Finished SNPs 701s Finished ref gaps 701s Finished read gaps 701s Mutated reference genome to subject genome 701s SNPs introduced: 30 701s Reference gaps introduced: 1 701s Read gaps introduced: 0 701s Rearrangements introduced: 0 701s Created read sampler 701s Sampling 90 reads 701s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 701s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 701s parsing sequence Sim.pm.1... 701s parsing sequence Sim.pm.2... 701s Parsed 234 reference bases 701s *** Run 71 of 100 701s /usr/bin/bowtie2 --cp-ival 1 --local --large-index -a --cp-min 4 --rfg 28.29134305509 -R 3 --score-min L,8.35790623837245,3.49169363025295 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 701s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 701s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '77' because it was < 2 characters long 701s Warning: skipping mate #2 of read '77' because it was < 2 characters long 701s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 701s Warning: skipping mate #2 of read '83' because it was < 2 characters long 701s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '85' because it was < 2 characters long 701s Read 50 alignments... 701s 90 reads; of these: 701s 90 (100.00%) were paired; of these: 701s 90 (100.00%) aligned concordantly 0 times 701s 0 (0.00%) aligned concordantly exactly 1 time 701s 0 (0.00%) aligned concordantly >1 times 701s ---- 701s 90 pairs aligned concordantly 0 times; of these: 701s 0 (0.00%) aligned discordantly 1 time 701s ---- 701s 90 pairs aligned 0 times concordantly or discordantly; of these: 701s 180 mates make up the pairs; of these: 701s 180 (100.00%) aligned 0 times 701s 0 (0.00%) aligned exactly 1 time 701s 0 (0.00%) aligned >1 times 701s 0.00% overall alignment rate 701s Read 100 alignments... 701s Read 150 alignments... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s Processing line... 701s --- Summary --- 701s Read 1 reference strings 701s Checked 0 alignments, 0 edits 701s --------------- 701s PASSED 701s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 701s /usr/bin/bowtie2 --cp-ival 1 --local --large-index -a --cp-min 4 --rfg 28.29134305509 -R 3 --score-min L,8.35790623837245,3.49169363025295 -q -p 3 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 701s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 701s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '77' because it was < 2 characters long 701s Warning: skipping mate #2 of read '77' because it was < 2 characters long 701s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 701s Warning: skipping mate #2 of read '83' because it was < 2 characters long 701s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 701s Warning: skipping mate #1 of read '85' because it was < 2 characters long 701s 90 reads; of these: 701s 90 (100.00%) were paired; of these: 701s 90 (100.00%) aligned concordantly 0 times 701s 0 (0.00%) aligned concordantly exactly 1 time 701s 0 (0.00%) aligned concordantly >1 times 701s ---- 701s 90 pairs aligned concordantly 0 times; of these: 701s 0 (0.00%) aligned discordantly 1 time 701s ---- 701s 90 pairs aligned 0 times concordantly or discordantly; of these: 701s 180 mates make up the pairs; of these: 701s 180 (100.00%) aligned 0 times 701s 0 (0.00%) aligned exactly 1 time 701s 0 (0.00%) aligned >1 times 701s 0.00% overall alignment rate 702s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 702s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 702s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 702s Flattened IUPAC characters 702s *** Run 72 of 100 702s /usr/bin/bowtie2 --cp-ival 1 --cp-min 5 --large-index --score-min L,4.16326964687459,5.28687989217452 --mp 4.44850822031647,4.21554855970742 -R 1 --gbar 3 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 702s Mutating sequence Sim.pm.1 702s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 702s Finished SNPs 702s Finished ref gaps 702s Finished read gaps 702s Mutating sequence Sim.pm.2 702s Introducing 20 SNPs, 0/1 ref/read gaps, and 1 rearrangements 702s Finished SNPs 702s Finished ref gaps 702s Finished read gaps 702s Mutated reference genome to subject genome 702s SNPs introduced: 24 702s Reference gaps introduced: 0 702s Read gaps introduced: 1 702s Rearrangements introduced: 2 702s Created read sampler 702s Sampling 40 reads 702s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 702s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 702s parsing sequence Sim.pm.1... 702s parsing sequence Sim.pm.2... 702s Parsed 234 reference bases 702s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 702s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 702s Warning: skipping read '21' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 702s 40 reads; of these: 702s 40 (100.00%) were unpaired; of these: 702s 32 (80.00%) aligned 0 times 702s 2 (5.00%) aligned exactly 1 time 702s 6 (15.00%) aligned >1 times 702s 20.00% overall alignment rate 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s GTTCGCCGTTCCCGGTGTGTC 702s GTTCGCCGTTCCCGGTGTGTC 702s Processing line... 702s TCG 702s TCG 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s CGTTCCCGGTGTGTCGTTGTAG 702s CGTTCCCGGTGTGTCGTTGTAG 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s ATGTCATCGC 702s ATGTCATCGC 702s Processing line... 702s GG 702s GG 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s TTCGCCGTTCCCGG 702s TTCGCCGTTCCCGG 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s GG 702s GG 702s Processing line... 702s Processing line... 702s GTAGGCCGTTGGGGTTCGCCGTTCC 702s GTAGGCCGTTGGGGTTCGCCGTTCC 702s Processing line... 702s --- Summary --- 702s Read 1 reference strings 702s Checked 8 alignments, 0 edits 702s --------------- 702s PASSED 702s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 702s /usr/bin/bowtie2 --cp-ival 1 --cp-min 5 --large-index --score-min L,4.16326964687459,5.28687989217452 --mp 4.44850822031647,4.21554855970742 -R 1 --gbar 3 -q -p 2 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 702s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 702s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 702s Warning: skipping read '21' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 702s 40 reads; of these: 702s 40 (100.00%) were unpaired; of these: 702s 32 (80.00%) aligned 0 times 702s 2 (5.00%) aligned exactly 1 time 702s 6 (15.00%) aligned >1 times 702s 20.00% overall alignment rate 702s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 702s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 702s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 702s /usr/bin/bowtie2 --cp-ival 1 --cp-min 5 --large-index --score-min L,4.16326964687459,5.28687989217452 --mp 4.44850822031647,4.21554855970742 -R 1 --gbar 3 -q -p 3 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 702s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 702s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 702s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 702s Warning: skipping read '21' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 702s 40 reads; of these: 702s 40 (100.00%) were unpaired; of these: 702s 32 (80.00%) aligned 0 times 702s 2 (5.00%) aligned exactly 1 time 702s 6 (15.00%) aligned >1 times 702s 20.00% overall alignment rate 702s Flattened IUPAC characters 702s Mutating sequence Sim.pm.2 702s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 702s Introducing 17 SNPs, 1/0 ref/read gaps, and 2 rearrangements 702s Finished SNPs 702s Finished ref gaps 702s Finished read gaps 702s Mutating sequence Sim.pm.1 702s Introducing 18 SNPs, 1/3 ref/read gaps, and 0 rearrangements 702s Finished SNPs 702s Finished ref gaps 702s Finished read gaps 702s Mutated reference genome to subject genome 702s SNPs introduced: 35 702s Reference gaps introduced: 2 702s Read gaps introduced: 3 702s Rearrangements introduced: 2 702s Created read sampler 702s Sampling 108 reads 702s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 702s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 702s parsing sequence Sim.pm.1... 702s parsing sequence Sim.pm.2... 702s Parsed 234 reference bases 702s *** Run 73 of 100 702s /usr/bin/bowtie2 --norc --trim5 8 --cp-min 2 -a --large-index --cp-ival 3 --local --mp 2.86017250507822,1.6141363867566 --score-min L,9.33944135431783,3.4890530708104 --mm -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw 702s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '0' because it was < 2 characters long 702s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '2' because it was < 2 characters long 702s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '6' because it was < 2 characters long 702s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '13' because it was < 2 characters long 702s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '17' because it was < 2 characters long 702s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '35' because it was < 2 characters long 702s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '36' because it was < 2 characters long 702s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '37' because it was < 2 characters long 702s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 702s Warning: skipping read '41' because it was < 2 characters long 702s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '43' because it was < 2 characters long 702s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 702s Warning: skipping read '49' because it was < 2 characters long 702s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '50' because it was < 2 characters long 702s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '62' because it was < 2 characters long 702s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '65' because it was < 2 characters long 702s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '77' because it was < 2 characters long 702s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '88' because it was < 2 characters long 702s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '89' because it was < 2 characters long 702s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '96' because it was < 2 characters long 702s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '99' because it was < 2 characters long 702s 108 reads; of these: 702s 108 (100.00%) were unpaired; of these: 702s 108 (100.00%) aligned 0 times 702s 0 (0.00%) aligned exactly 1 time 702s 0 (0.00%) aligned >1 times 702s 0.00% overall alignment rate 702s Read 50 alignments... 702s Read 100 alignments... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s *** Run 74 of 100 702s /usr/bin/bowtie2 --cp-min 2 --large-index --n-ceil 1.23751794392663,0.221945960244819 --trim5 9 --cp-ival 1 --trim3 4 --score-min L,1.54591271299989,8.572648619616 -i C,0.521118340219864,9.33434159095354 --rdg 45.7638026685097,13.3265828940829 -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s --- Summary --- 702s Read 1 reference strings 702s Checked 0 alignments, 0 edits 702s --------------- 702s PASSED 702s Flattened IUPAC characters 702s Mutating sequence Sim.pm.2 702s Introducing 7 SNPs, 0/1 ref/read gaps, and 2 rearrangements 702s Finished SNPs 702s Finished ref gaps 702s Finished read gaps 702s Mutating sequence Sim.pm.1 702s Introducing 17 SNPs, 2/0 ref/read gaps, and 0 rearrangements 702s Finished SNPs 702s Finished ref gaps 702s Finished read gaps 702s Mutated reference genome to subject genome 702s SNPs introduced: 24 702s Reference gaps introduced: 2 702s Read gaps introduced: 1 702s Rearrangements introduced: 2 702s Created read sampler 702s Sampling 43 reads 702s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 702s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 702s parsing sequence Sim.pm.1... 702s parsing sequence Sim.pm.2... 702s Parsed 234 reference bases 702s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 702s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '1' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 702s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '5' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 702s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '9' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 702s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '11' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 702s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '12' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 702s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '14' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 702s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '23' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 702s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '31' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 702s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '35' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 702s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '37' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 702s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '39' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 702s 43 reads; of these: 702s 43 (100.00%) were unpaired; of these: 702s 39 (90.70%) aligned 0 times 702s 3 (6.98%) aligned exactly 1 time 702s 1 (2.33%) aligned >1 times 702s 9.30% overall alignment rate 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s GCCAGTTCGATTC 702s GCCAGTTCGATTC 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s GG 702s GG 702s Processing line... 702s Processing line... 702s Processing line... 702s TTGGTTTATGTCATCG 702s TTGGTTTATGTCATCG 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s CGCGCGGTTGTTTGG 702s CGCGCGGTTGTTTGG 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s --- Summary --- 702s Read 1 reference strings 702s Checked 4 alignments, 0 edits 702s --------------- 702s PASSED 702s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 702s /usr/bin/bowtie2 --cp-min 2 --large-index --n-ceil 1.23751794392663,0.221945960244819 --trim5 9 --cp-ival 1 --trim3 4 --score-min L,1.54591271299989,8.572648619616 -i C,0.521118340219864,9.33434159095354 --rdg 45.7638026685097,13.3265828940829 -r -p 3 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 702s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 702s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '1' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 702s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '5' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 702s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '9' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 702s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '11' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 702s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '12' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 702s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '14' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 702s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '23' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 702s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '35' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 702s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '37' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 702s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '39' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 702s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '31' because it was < 2 characters long 702s 43 reads; of these: 702s 43 (100.00%) were unpaired; of these: 702s 39 (90.70%) aligned 0 times 702s 3 (6.98%) aligned exactly 1 time 702s 1 (2.33%) aligned >1 times 702s 9.30% overall alignment rate 702s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 702s Flattened IUPAC characters 702s Mutating sequence Sim.pm.1 702s Introducing 9 SNPs, 1/0 ref/read gaps, and 0 rearrangements 702s Finished SNPs 702s Finished ref gaps 702s Finished read gaps 702s Mutating sequence Sim.pm.2 702s Introducing 19 SNPs, 0/1 ref/read gaps, and 0 rearrangements 702s Finished SNPs 702s Finished ref gaps 702s Finished read gaps 702s Mutated reference genome to subject genome 702s SNPs introduced: 28 702s Reference gaps introduced: 1 702s Read gaps introduced: 1 702s Rearrangements introduced: 0 702s Created read sampler 702s Sampling 94 reads 702s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 702s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 702s parsing sequence Sim.pm.1... 702s parsing sequence Sim.pm.2... 702s Parsed 234 reference bases 702s *** Run 75 of 100 702s /usr/bin/bowtie2 --cp-min 7 --large-index --ma 20.0578543240752 --score-min L,5.22962422832756,1.18544784223804 -R 1 --gbar 1 -D 10 --cp-ival 1 -M 3 --trim5 4 --rfg 46.7890703841443 --mp 9.98704167776673,7.07970720146555 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 702s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 702s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 702s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '11' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 702s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '18' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 702s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '23' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 702s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '39' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 702s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '53' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 702s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '54' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 702s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '57' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 702s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '60' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 702s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '76' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 702s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '77' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 702s Read 50 alignments... 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 702s Warning: skipping mate #1 of read '91' because length (1) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '91' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 702s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '92' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 702s 94 reads; of these: 702s 86 (91.49%) were paired; of these: 702s 84 (97.67%) aligned concordantly 0 times 702s 0 (0.00%) aligned concordantly exactly 1 time 702s 2 (2.33%) aligned concordantly >1 times 702s ---- 702s 84 pairs aligned concordantly 0 times; of these: 702s 0 (0.00%) aligned discordantly 1 time 702s ---- 702s 84 pairs aligned 0 times concordantly or discordantly; of these: 702s 168 mates make up the pairs; of these: 702s 145 (86.31%) aligned 0 times 702s 12 (7.14%) aligned exactly 1 time 702s 11 (6.55%) aligned >1 times 702s 8 (8.51%) were unpaired; of these: 702s 6 (75.00%) aligned 0 times 702s 0 (0.00%) aligned exactly 1 time 702s 2 (25.00%) aligned >1 times 702s 16.11% overall alignment rate 702s Read 100 alignments... 702s Read 150 alignments... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s TAT 702s TAT 702s Processing line... 702s GTGCGGCGGGGCCAG 702s GTGCGGCGGGGCCAG 702s Processing line... 702s CGTTGTAGGCCGTTGGGGTTCGCCGTTC 702s CGTTGTAGGCCGTTGGGGTTCGCCGTTC 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s GTTTATGTC 702s GTTTATGTC 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s AGTTCGATTCGGTTGGTTTATGTCATCGC 702s AGTTCGATTCGGTTGGTTTATGTCATCGC 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s CG 702s CG 702s Processing line... 702s Processing line... 702s GGGGCGTGGGTGCGGCGGG 702s GGGGCGTGGGTGCGGCGGG 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s TTCGGTTGGT 702s TTCGGTTGGT 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s GTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCCC 702s GTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCCC 702s Processing line... 702s Processing line... 702s GCGGCGGG 702s GCGGCGGG 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s GGTGTGTCGTTG 702s GGTGTGTCGTTG 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s CGGTGTGTCGTTGTAGGCCGTTGGG 702s CGGTGTGTCGTTGTAGGCCGTTGGG 702s Processing line... 702s Processing line... 702s CG 702s CG 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s CGGT 702s CGGT 702s Processing line... 702s GTGTGTC 702s GTGTGTC 702s Processing line... 702s GC 702s GC 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s TTC 702s TTC 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s CCGTT 702s CCGTT 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s CCCGGTGTG 702s CCCGGTGTG 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s TTGTAGGCCGTTGGGGTTCCC 702s TTGTAGGCCGTTGGGGTTCCC 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s CGGCCCGTT 702s CGGCCCGTT 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s GGTGCGGCGGGGCCAGT 702s GGTGCGGCGGGGCCAGT 702s Processing line... 702s Processing line... 702s CGT 702s CGT 702s Processing line... 702s Processing line... 702s GG 702s GG 702s Processing line... 702s AGGTTGGAGTCCCGCGG 702s AGGTTGGAGTCCCGCGG 702s Processing line... 702s Processing line... 702s GTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTC 702s GTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTC 702s Processing line... 702s Processing line... 702s TG 702s TG 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s CGT 702s CGT 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s Processing line... 702s CGTTGGGGTTCGCCGTTCCCGGT 702s CGTTGGGGTTCGCCGTTCCCGGT 702s Processing line... 702s --- Summary --- 702s Read 1 reference strings 702s Checked 29 alignments, 0 edits 702s --------------- 702s PASSED 702s ALSO checking that bowtie2 and bowtie2-align match up 702s /usr/bin/bowtie2 --cp-min 7 --large-index --ma 20.0578543240752 --score-min L,5.22962422832756,1.18544784223804 -R 1 --gbar 1 -D 10 --cp-ival 1 -M 3 --trim5 4 --rfg 46.7890703841443 --mp 9.98704167776673,7.07970720146555 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 702s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 702s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 702s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '11' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 702s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '18' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 702s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '23' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 702s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '39' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 702s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 702s /usr/bin/bowtie2 --cp-min 7 --large-index --ma 20.0578543240752 --score-min L,5.22962422832756,1.18544784223804 -R 1 --gbar 1 -D 10 --cp-ival 1 -M 3 --trim5 4 --rfg 46.7890703841443 --mp 9.98704167776673,7.07970720146555 -q -p 3 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 702s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '53' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 702s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '54' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 702s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '57' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 702s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '60' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 702s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '76' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 702s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '77' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 702s Warning: skipping mate #1 of read '91' because length (1) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '91' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 702s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '92' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 702s 94 reads; of these: 702s 86 (91.49%) were paired; of these: 702s 84 (97.67%) aligned concordantly 0 times 702s 0 (0.00%) aligned concordantly exactly 1 time 702s 2 (2.33%) aligned concordantly >1 times 702s ---- 702s 84 pairs aligned concordantly 0 times; of these: 702s 0 (0.00%) aligned discordantly 1 time 702s ---- 702s 84 pairs aligned 0 times concordantly or discordantly; of these: 702s 168 mates make up the pairs; of these: 702s 145 (86.31%) aligned 0 times 702s 12 (7.14%) aligned exactly 1 time 702s 11 (6.55%) aligned >1 times 702s 8 (8.51%) were unpaired; of these: 702s 6 (75.00%) aligned 0 times 702s 0 (0.00%) aligned exactly 1 time 702s 2 (25.00%) aligned >1 times 702s 16.11% overall alignment rate 702s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 702s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 702s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 702s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '11' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 702s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '18' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 702s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '23' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 702s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '39' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 702s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '53' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 702s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '54' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 702s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '57' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 702s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '60' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 702s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '76' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 702s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '77' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 702s Warning: skipping mate #1 of read '91' because length (1) <= # seed mismatches (0) 702s Warning: skipping mate #1 of read '91' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 702s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 702s Warning: skipping read '92' because it was < 2 characters long 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 702s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 702s 94 reads; of these: 702s 86 (91.49%) were paired; of these: 702s 84 (97.67%) aligned concordantly 0 times 702s 0 (0.00%) aligned concordantly exactly 1 time 702s 2 (2.33%) aligned concordantly >1 times 702s ---- 702s 84 pairs aligned concordantly 0 times; of these: 702s 0 (0.00%) aligned discordantly 1 time 702s ---- 702s 84 pairs aligned 0 times concordantly or discordantly; of these: 702s 168 mates make up the pairs; of these: 702s 145 (86.31%) aligned 0 times 702s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 702s 12 (7.14%) aligned exactly 1 time 702s 11 (6.55%) aligned >1 times 702s 8 (8.51%) were unpaired; of these: 702s 6 (75.00%) aligned 0 times 702s 0 (0.00%) aligned exactly 1 time 702s 2 (25.00%) aligned >1 times 702s 16.11% overall alignment rate 702s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 702s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 702s Flattened IUPAC characters 702s Mutating sequence Sim.pm.1 702s Introducing 10 SNPs, 3/2 ref/read gaps, and 1 rearrangements 702s Finished SNPs 702s Finished ref gaps 702s Finished read gaps 702s Mutating sequence Sim.pm.2 702s Introducing 17 SNPs, 1/0 ref/read gaps, and 0 rearrangements 702s Finished SNPs 702s Finished ref gaps 702s Finished read gaps 702s Mutated reference genome to subject genome 702s SNPs introduced: 27 702s Reference gaps introduced: 4 702s Read gaps introduced: 2 702s Rearrangements introduced: 1 702s Created read sampler 702s Sampling 52 reads 702s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 703s *** Run 76 of 100 703s /usr/bin/bowtie2 --large-index --cp-min 2 --cp-ival 1 -D 27 -R 1 --mp 8.41968273635629,5.35432405309637 --score-min L,1.51517929033853,5.9964020222864 --nofw --rfg 45.2485746658076,1.14334658169395 -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw 703s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 703s parsing sequence Sim.pm.1... 703s parsing sequence Sim.pm.2... 703s Parsed 234 reference bases 703s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 703s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 703s Warning: skipping read '39' because it was < 2 characters long 703s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 703s 52 reads; of these: 703s 52 (100.00%) were unpaired; of these: 703s 46 (88.46%) aligned 0 times 703s 1 (1.92%) aligned exactly 1 time 703s 5 (9.62%) aligned >1 times 703s 11.54% overall alignment rate 703s Read 50 alignments... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s /usr/bin/bowtie2 --large-index --cp-min 2 --cp-ival 1 -D 27 -R 1 --mp 8.41968273635629,5.35432405309637 --score-min L,1.51517929033853,5.9964020222864 --nofw --rfg 45.2485746658076,1.14334658169395 -r -p 4 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s GCCGT 703s GCCGT 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s TTCCCGGTGTGTCGTTG 703s TTCCCGGTGTGTCGTTG 703s Processing line... 703s Processing line... 703s GTG 703s GTG 703s Processing line... 703s Processing line... 703s GG 703s GG 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s ATCGCGCGG 703s ATCGCGCGG 703s Processing line... 703s Processing line... 703s Processing line... 703s GCGGGG 703s GCGGGG 703s Processing line... 703s Processing line... 703s --- Summary --- 703s Read 1 reference strings 703s Checked 6 alignments, 0 edits 703s --------------- 703s PASSED 703s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 703s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 703s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 703s Warning: skipping read '39' because it was < 2 characters long 703s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 703s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 703s 52 reads; of these: 703s 52 (100.00%) were unpaired; of these: 703s 46 (88.46%) aligned 0 times 703s 1 (1.92%) aligned exactly 1 time 703s 5 (9.62%) aligned >1 times 703s 11.54% overall alignment rate 703s Flattened IUPAC characters 703s Mutating sequence Sim.pm.1 703s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 703s Finished SNPs 703s Finished ref gaps 703s Finished read gaps 703s Mutating sequence Sim.pm.2 703s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 703s Finished SNPs 703s Finished ref gaps 703s Finished read gaps 703s Mutated reference genome to subject genome 703s SNPs introduced: 1 703s Reference gaps introduced: 1 703s Read gaps introduced: 1 703s Rearrangements introduced: 1 703s Created read sampler 703s Sampling 57 reads 703s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 703s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 703s parsing sequence Sim.pm.1... 703s parsing sequence Sim.pm.2... 703s Parsed 234 reference bases 703s *** Run 77 of 100 703s /usr/bin/bowtie2 -i C,2.03922531489942 --mp 2.81651506731463,2.58908025877169 --nofw --trim3 0 --trim5 3 --cp-ival 2 --local -k 3 -D 22 --score-min L,1.8710546540281,8.93801897844841 --mm --rdg 23.9214174595291 --cp-min 7 --np 5 --large-index -f -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta 703s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 703s Warning: skipping read '8' because it was < 2 characters long 703s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 703s Warning: skipping read '21' because it was < 2 characters long 703s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 703s Warning: skipping read '32' because it was < 2 characters long 703s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 703s Warning: skipping read '41' because it was < 2 characters long 703s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 703s Warning: skipping read '54' because it was < 2 characters long 703s 57 reads; of these: 703s 57 (100.00%) were unpaired; of these: 703s 57 (100.00%) aligned 0 times 703s 0 (0.00%) aligned exactly 1 time 703s 0 (0.00%) aligned >1 times 703s 0.00% overall alignment rate 703s Read 50 alignments... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s /usr/bin/bowtie2 -i C,2.03922531489942 --mp 2.81651506731463,2.58908025877169 --nofw --trim3 0 --trim5 3 --cp-ival 2 --local -k 3 -D 22 --score-min L,1.8710546540281,8.93801897844841 --mm --rdg 23.9214174595291 --cp-min 7 --np 5 --large-index -f -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s --- Summary --- 703s Read 1 reference strings 703s Checked 0 alignments, 0 edits 703s --------------- 703s PASSED 703s ALSO checking that bowtie2 and bowtie2-align match up 703s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 703s Warning: skipping read '8' because it was < 2 characters long 703s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 703s Warning: skipping read '21' because it was < 2 characters long 703s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 703s Warning: skipping read '32' because it was < 2 characters long 703s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 703s Warning: skipping read '41' because it was < 2 characters long 703s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 703s Warning: skipping read '54' because it was < 2 characters long 703s 57 reads; of these: 703s 57 (100.00%) were unpaired; of these: 703s 57 (100.00%) aligned 0 times 703s 0 (0.00%) aligned exactly 1 time 703s 0 (0.00%) aligned >1 times 703s 0.00% overall alignment rate 703s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 703s Flattened IUPAC characters 703s Mutating sequence Sim.pm.1 703s Introducing 8 SNPs, 1/3 ref/read gaps, and 0 rearrangements 703s Finished SNPs 703s Finished ref gaps 703s Finished read gaps 703s Mutating sequence Sim.pm.2 703s Introducing 14 SNPs, 2/0 ref/read gaps, and 1 rearrangements 703s Finished SNPs 703s Finished ref gaps 703s Finished read gaps 703s Mutated reference genome to subject genome 703s SNPs introduced: 22 703s Reference gaps introduced: 3 703s Read gaps introduced: 3 703s Rearrangements introduced: 1 703s Created read sampler 703s Sampling 164 reads 703s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 703s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 703s parsing sequence Sim.pm.1... 703s parsing sequence Sim.pm.2... 703s Parsed 234 reference bases 703s *** Run 78 of 100 703s /usr/bin/bowtie2 --large-index --np 2 --cp-min 7 --rdg 39.0879751660293,11.8925203000494 -D 20 --gbar 4 -R 4 --score-min L,9.14799103400635,8.1993297813195 --cp-ival 1 --local --trim5 4 -M 2 -N 1 -L16 --trim3 4 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 703s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 703s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #2 of read '3' because it was < 2 characters long 703s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '5' because it was < 2 characters long 703s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '6' because it was < 2 characters long 703s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '9' because it was < 2 characters long 703s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '19' because it was < 2 characters long 703s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '35' because it was < 2 characters long 703s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '36' because it was < 2 characters long 703s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '38' because it was < 2 characters long 703s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '48' because it was < 2 characters long 703s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #2 of read '49' because it was < 2 characters long 703s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '55' because it was < 2 characters long 703s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '64' because it was < 2 characters long 703s Read 50 alignments... 703s Read 100 alignments... 703s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '68' because it was < 2 characters long 703s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 703s Warning: skipping read '73' because it was < 2 characters long 703s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '82' because it was < 2 characters long 703s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '84' because it was < 2 characters long 703s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '96' because it was < 2 characters long 703s Warning: skipping mate #1 of read '97' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '97' because it was < 2 characters long 703s Warning: skipping mate #2 of read '100' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #2 of read '100' because it was < 2 characters long 703s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '101' because it was < 2 characters long 703s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '103' because it was < 2 characters long 703s Warning: skipping mate #2 of read '115' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #2 of read '115' because it was < 2 characters long 703s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 703s Warning: skipping read '125' because it was < 2 characters long 703s Warning: skipping read '137' because length (0) <= # seed mismatches (1) 703s Warning: skipping read '137' because it was < 2 characters long 703s Read 150 alignments... 703s Read 200 alignments... 703s Warning: skipping mate #1 of read '145' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '145' because it was < 2 characters long 703s Warning: skipping mate #1 of read '153' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '153' because it was < 2 characters long 703s 164 reads; of these: 703s 132 (80.49%) were paired; of these: 703s 132 (100.00%) aligned concordantly 0 times 703s 0 (0.00%) aligned concordantly exactly 1 time 703s 0 (0.00%) aligned concordantly >1 times 703s ---- 703s 132 pairs aligned concordantly 0 times; of these: 703s 0 (0.00%) aligned discordantly 1 time 703s ---- 703s 132 pairs aligned 0 times concordantly or discordantly; of these: 703s 264 mates make up the pairs; of these: 703s 264 (100.00%) aligned 0 times 703s 0 (0.00%) aligned exactly 1 time 703s 0 (0.00%) aligned >1 times 703s 32 (19.51%) were unpaired; of these: 703s 32 (100.00%) aligned 0 times 703s 0 (0.00%) aligned exactly 1 time 703s 0 (0.00%) aligned >1 times 703s 0.00% overall alignment rate 703s Read 250 alignments... 703s Read 300 alignments... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s /usr/bin/bowtie2 --large-index --np 2 --cp-min 7 --rdg 39.0879751660293,11.8925203000494 -D 20 --gbar 4 -R 4 --score-min L,9.14799103400635,8.1993297813195 --cp-ival 1 --local --trim5 4 -M 2 -N 1 -L16 --trim3 4 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s --- Summary --- 703s Read 1 reference strings 703s Checked 0 alignments, 0 edits 703s --------------- 703s PASSED 703s ALSO checking that bowtie2 and bowtie2-align match up 703s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 703s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #2 of read '3' because it was < 2 characters long 703s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '5' because it was < 2 characters long 703s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '6' because it was < 2 characters long 703s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '9' because it was < 2 characters long 703s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '19' because it was < 2 characters long 703s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '35' because it was < 2 characters long 703s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '36' because it was < 2 characters long 703s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '38' because it was < 2 characters long 703s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '48' because it was < 2 characters long 703s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #2 of read '49' because it was < 2 characters long 703s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '55' because it was < 2 characters long 703s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '64' because it was < 2 characters long 703s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '68' because it was < 2 characters long 703s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 703s Warning: skipping read '73' because it was < 2 characters long 703s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '82' because it was < 2 characters long 703s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '84' because it was < 2 characters long 703s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '96' because it was < 2 characters long 703s Warning: skipping mate #1 of read '97' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '97' because it was < 2 characters long 703s Warning: skipping mate #2 of read '100' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #2 of read '100' because it was < 2 characters long 703s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '101' because it was < 2 characters long 703s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '103' because it was < 2 characters long 703s Warning: skipping mate #2 of read '115' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #2 of read '115' because it was < 2 characters long 703s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 703s Warning: skipping read '125' because it was < 2 characters long 703s Warning: skipping read '137' because length (0) <= # seed mismatches (1) 703s Warning: skipping read '137' because it was < 2 characters long 703s Warning: skipping mate #1 of read '145' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '145' because it was < 2 characters long 703s Warning: skipping mate #1 of read '153' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '153' because it was < 2 characters long 703s 164 reads; of these: 703s 132 (80.49%) were paired; of these: 703s 132 (100.00%) aligned concordantly 0 times 703s 0 (0.00%) aligned concordantly exactly 1 time 703s 0 (0.00%) aligned concordantly >1 times 703s ---- 703s 132 pairs aligned concordantly 0 times; of these: 703s 0 (0.00%) aligned discordantly 1 time 703s ---- 703s 132 pairs aligned 0 times concordantly or discordantly; of these: 703s 264 mates make up the pairs; of these: 703s 264 (100.00%) aligned 0 times 703s 0 (0.00%) aligned exactly 1 time 703s 0 (0.00%) aligned >1 times 703s 32 (19.51%) were unpaired; of these: 703s 32 (100.00%) aligned 0 times 703s 0 (0.00%) aligned exactly 1 time 703s 0 (0.00%) aligned >1 times 703s 0.00% overall alignment rate 703s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 703s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 703s /usr/bin/bowtie2 --large-index --np 2 --cp-min 7 --rdg 39.0879751660293,11.8925203000494 -D 20 --gbar 4 -R 4 --score-min L,9.14799103400635,8.1993297813195 --cp-ival 1 --local --trim5 4 -M 2 -N 1 -L16 --trim3 4 -q -p 3 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 703s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 703s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #2 of read '3' because it was < 2 characters long 703s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '5' because it was < 2 characters long 703s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '6' because it was < 2 characters long 703s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '9' because it was < 2 characters long 703s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '19' because it was < 2 characters long 703s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '35' because it was < 2 characters long 703s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '36' because it was < 2 characters long 703s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '38' because it was < 2 characters long 703s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '48' because it was < 2 characters long 703s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #2 of read '49' because it was < 2 characters long 703s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '55' because it was < 2 characters long 703s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '64' because it was < 2 characters long 703s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '68' because it was < 2 characters long 703s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 703s Warning: skipping read '73' because it was < 2 characters long 703s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '82' because it was < 2 characters long 703s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '84' because it was < 2 characters long 703s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '96' because it was < 2 characters long 703s Warning: skipping mate #1 of read '97' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '97' because it was < 2 characters long 703s Warning: skipping mate #2 of read '100' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #2 of read '100' because it was < 2 characters long 703s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '101' because it was < 2 characters long 703s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '103' because it was < 2 characters long 703s Warning: skipping mate #2 of read '115' because length (1) <= # seed mismatches (1) 703s Warning: skipping mate #2 of read '115' because it was < 2 characters long 703s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 703s Warning: skipping read '125' because it was < 2 characters long 703s Warning: skipping read '137' because length (0) <= # seed mismatches (1) 703s Warning: skipping read '137' because it was < 2 characters long 703s Warning: skipping mate #1 of read '145' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '145' because it was < 2 characters long 703s Warning: skipping mate #1 of read '153' because length (0) <= # seed mismatches (1) 703s Warning: skipping mate #1 of read '153' because it was < 2 characters long 703s 164 reads; of these: 703s 132 (80.49%) were paired; of these: 703s 132 (100.00%) aligned concordantly 0 times 703s 0 (0.00%) aligned concordantly exactly 1 time 703s 0 (0.00%) aligned concordantly >1 times 703s ---- 703s 132 pairs aligned concordantly 0 times; of these: 703s 0 (0.00%) aligned discordantly 1 time 703s ---- 703s 132 pairs aligned 0 times concordantly or discordantly; of these: 703s 264 mates make up the pairs; of these: 703s 264 (100.00%) aligned 0 times 703s 0 (0.00%) aligned exactly 1 time 703s 0 (0.00%) aligned >1 times 703s 32 (19.51%) were unpaired; of these: 703s 32 (100.00%) aligned 0 times 703s 0 (0.00%) aligned exactly 1 time 703s 0 (0.00%) aligned >1 times 703s 0.00% overall alignment rate 703s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 703s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 703s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 703s Flattened IUPAC characters 703s Mutating sequence Sim.pm.2 703s Introducing 12 SNPs, 2/0 ref/read gaps, and 2 rearrangements 703s Finished SNPs 703s Finished ref gaps 703s Finished read gaps 703s Mutating sequence Sim.pm.1 703s Introducing 10 SNPs, 1/2 ref/read gaps, and 2 rearrangements 703s Finished SNPs 703s Finished ref gaps 703s Finished read gaps 703s Mutated reference genome to subject genome 703s SNPs introduced: 22 703s Reference gaps introduced: 3 703s Read gaps introduced: 2 703s Rearrangements introduced: 4 703s Created read sampler 703s Sampling 17 reads 703s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 703s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 703s parsing sequence Sim.pm.1... 703s parsing sequence Sim.pm.2... 703s Parsed 234 reference bases 703s *** Run 79 of 100 703s /usr/bin/bowtie2 --rdg 28.504617809268 --rfg 40.87329674616 --score-min L,9.07647977652996,1.42540755735694 --trim3 8 --cp-ival 1 --large-index --cp-min 5 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 703s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 703s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 703s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 703s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 703s Warning: skipping mate #2 of read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 703s Warning: skipping mate #2 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 703s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 703s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 703s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 703s 17 reads; of these: 703s 16 (94.12%) were paired; of these: 703s 16 (100.00%) aligned concordantly 0 times 703s 0 (0.00%) aligned concordantly exactly 1 time 703s 0 (0.00%) aligned concordantly >1 times 703s ---- 703s 16 pairs aligned concordantly 0 times; of these: 703s 0 (0.00%) aligned discordantly 1 time 703s ---- 703s 16 pairs aligned 0 times concordantly or discordantly; of these: 703s 32 mates make up the pairs; of these: 703s 28 (87.50%) aligned 0 times 703s 1 (3.12%) aligned exactly 1 time 703s 3 (9.38%) aligned >1 times 703s 1 (5.88%) were unpaired; of these: 703s 1 (100.00%) aligned 0 times 703s 0 (0.00%) aligned exactly 1 time 703s 0 (0.00%) aligned >1 times 703s 12.12% overall alignment rate 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s CGGTGTGTCGTTGTA 703s CGGTGTGTCGTTGTA 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s CCGGTG 703s CCGGTG 703s Processing line... 703s Processing line... 703s TTCCCGGT 703s TTCCCGGT 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s Processing line... 703s TCTCAGGTTGGAG 703s TCTCAGGTTGGAG 703s Processing line... 703s --- Summary --- 703s Read 1 reference strings 703s Checked 4 alignments, 0 edits 703s --------------- 703s PASSED 703s Flattened IUPAC characters 703s Mutating sequence Sim.pm.1 703s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 703s Finished SNPs 703s Finished ref gaps 703s Finished read gaps 703s Mutating sequence Sim.pm.2 703s Introducing 13 SNPs, 0/1 ref/read gaps, and 0 rearrangements 703s Finished SNPs 703s Finished ref gaps 703s Finished read gaps 703s Mutated reference genome to subject genome 703s SNPs introduced: 16 703s Reference gaps introduced: 0 703s Read gaps introduced: 1 703s Rearrangements introduced: 1 703s Created read sampler 703s Sampling 59 reads 703s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 703s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 703s parsing sequence Sim.pm.1... 703s parsing sequence Sim.pm.2... 703s Parsed 234 reference bases 703s *** Run 80 of 100 703s /usr/bin/bowtie2 --trim5 7 --n-ceil 0.995553695886426,0.796229884810532 --cp-min 3 --large-index --cp-ival 3 --local -N 0 -L19 -R 2 --score-min L,7.98890821684953,2.69183452092387 --mm --rdg 12.4472578587089,14.3071997403689 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 704s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '3' because it was < 2 characters long 704s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '9' because it was < 2 characters long 704s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '13' because it was < 2 characters long 704s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '28' because it was < 2 characters long 704s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '47' because it was < 2 characters long 704s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '50' because it was < 2 characters long 704s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '56' because it was < 2 characters long 704s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '59' because it was < 2 characters long 704s 59 reads; of these: 704s 59 (100.00%) were unpaired; of these: 704s 59 (100.00%) aligned 0 times 704s 0 (0.00%) aligned exactly 1 time 704s 0 (0.00%) aligned >1 times 704s 0.00% overall alignment rate 704s Read 50 alignments... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s --- Summary --- 704s Read 1 reference strings 704s Checked 0 alignments, 0 edits 704s --------------- 704s PASSED 704s Flattened IUPAC characters 704s Mutating sequence Sim.pm.1 704s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 704s Finished SNPs 704s Finished ref gaps 704s Finished read gaps 704s Mutating sequence Sim.pm.2 704s Introducing 28 SNPs, 0/0 ref/read gaps, and 2 rearrangements 704s Finished SNPs 704s Finished ref gaps 704s Finished read gaps 704s Mutated reference genome to subject genome 704s SNPs introduced: 34 704s Reference gaps introduced: 0 704s Read gaps introduced: 1 704s Rearrangements introduced: 2 704s Created read sampler 704s Sampling 39 reads 704s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 704s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 704s parsing sequence Sim.pm.1... 704s parsing sequence Sim.pm.2... 704s Parsed 234 reference bases 704s *** Run 81 of 100 704s /usr/bin/bowtie2 --np 3 --cp-min 2 --large-index --ma 30.7100994020507 --score-min L,3.97153854955955,4.79111705499 --mm --rdg 1.25090414440578,15.7634509917783 -M 5 --cp-ival 1 --nofw -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 704s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 704s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 704s Warning: skipping mate #1 of read '33' because length (1) <= # seed mismatches (0) 704s Warning: skipping mate #1 of read '33' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 704s 39 reads; of these: 704s 39 (100.00%) were paired; of these: 704s 39 (100.00%) aligned concordantly 0 times 704s 0 (0.00%) aligned concordantly exactly 1 time 704s 0 (0.00%) aligned concordantly >1 times 704s ---- 704s 39 pairs aligned concordantly 0 times; of these: 704s 0 (0.00%) aligned discordantly 1 time 704s ---- 704s 39 pairs aligned 0 times concordantly or discordantly; of these: 704s 78 mates make up the pairs; of these: 704s 69 (88.46%) aligned 0 times 704s 1 (1.28%) aligned exactly 1 time 704s 8 (10.26%) aligned >1 times 704s 11.54% overall alignment rate 704s Read 50 alignments... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAG 704s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAG 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s GGTTCGCCGTT 704s GGTTCGCCGTT 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s GT 704s GT 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s GG 704s GG 704s Processing line... 704s Processing line... 704s CGG 704s CGG 704s Processing line... 704s Processing line... 704s GGTGTGTCGTT 704s GGTGTGTCGTT 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s CG 704s CG 704s Processing line... 704s Processing line... 704s CGTTGTA 704s CGTTGTA 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s /usr/bin/bowtie2 --np 3 --cp-min 2 --large-index --ma 30.7100994020507 --score-min L,3.97153854955955,4.79111705499 --mm --rdg 1.25090414440578,15.7634509917783 -M 5 --cp-ival 1 --nofw -r -p 3 -x /tmp/Sim.pm.RKKEKvBt --reorder -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s GGTGACGCCGTTGAACGTGCGGCGGGGCCA 704s GGTGACGCCGTTGAACGTGCGGCGGGGCCA 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s --- Summary --- 704s Read 1 reference strings 704s Checked 9 alignments, 0 edits 704s --------------- 704s PASSED 704s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 704s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 704s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 704s Warning: skipping mate #1 of read '33' because length (1) <= # seed mismatches (0) 704s Warning: skipping mate #1 of read '33' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 704s 39 reads; of these: 704s 39 (100.00%) were paired; of these: 704s 39 (100.00%) aligned concordantly 0 times 704s 0 (0.00%) aligned concordantly exactly 1 time 704s 0 (0.00%) aligned concordantly >1 times 704s ---- 704s 39 pairs aligned concordantly 0 times; of these: 704s 0 (0.00%) aligned discordantly 1 time 704s ---- 704s 39 pairs aligned 0 times concordantly or discordantly; of these: 704s 78 mates make up the pairs; of these: 704s 69 (88.46%) aligned 0 times 704s 1 (1.28%) aligned exactly 1 time 704s 8 (10.26%) aligned >1 times 704s 11.54% overall alignment rate 704s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 704s Flattened IUPAC characters 704s Mutating sequence Sim.pm.1 704s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 704s Finished SNPs 704s Finished ref gaps 704s Finished read gaps 704s Mutating sequence Sim.pm.2 704s Introducing 7 SNPs, 1/2 ref/read gaps, and 1 rearrangements 704s Finished SNPs 704s Finished ref gaps 704s Finished read gaps 704s Mutated reference genome to subject genome 704s SNPs introduced: 7 704s Reference gaps introduced: 2 704s Read gaps introduced: 2 704s Rearrangements introduced: 2 704s Created read sampler 704s Sampling 103 reads 704s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 704s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 704s parsing sequence Sim.pm.1... 704s parsing sequence Sim.pm.2... 704s Parsed 234 reference bases 704s *** Run 82 of 100 704s /usr/bin/bowtie2 -D 20 --gbar 2 --score-min L,7.71077271151155,1.36210382207242 --mm --cp-min 4 --np 2 --large-index --mp 5.51213249309513,2.78592040287481 --trim3 9 -a --cp-ival 1 --local --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq 704s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (1) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 704s 103 reads; of these: 704s 103 (100.00%) were unpaired; of these: 704s 80 (77.67%) aligned 0 times 704s 18 (17.48%) aligned exactly 1 time 704s 5 (4.85%) aligned >1 times 704s 22.33% overall alignment rate 704s Read 50 alignments... 704s Read 100 alignments... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s CCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCC 704s CCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTT---C 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s TGGAGTCCCGCGGCCCTTTAGGTAGCGGACTGGTGACGCCGTTGAACGTGCGGCGGGGCCAGTT 704s TGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCGGCGGGGCCAG-T 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCG 704s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCG 704s Processing line... 704s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCG 704s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCG 704s Processing line... 704s GGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATTTCATCGCGCGGTTGTTTGGTGTGGACGGG 704s GGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNC-GG 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s TCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCG 704s TCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCG 704s Processing line... 704s TCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGC 704s TCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC-C 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s CGGCGGGGCCAGTTCGA 704s CGGCGGGGCCAGTTCGA 704s Processing line... 704s Processing line... 704s Processing line... 704s TTGTTTGGTGT 704s TTGTTTGGTGT 704s Processing line... 704s Processing line... 704s GGGCGTGGGTGCGGCGGGGC 704s GGGCGTGGGTGCGGCGGGGC 704s Processing line... 704s Processing line... 704s Processing line... 704s GGTGTGGACGGGGGTCTCAGGTTGGAGTCC 704s GGTGTGTNCGGGGGTCTCAGGTTGGAGTCC 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s GGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATTTCATCGCGCGGTTGTTTGGTGTGGACGGGGGTCTC 704s GGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTC 704s Processing line... 704s Processing line... 704s TCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGT 704s TCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGT 704s Processing line... 704s Processing line... 704s TCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCG 704s TCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCG 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s GTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGG 704s GTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGG 704s Processing line... 704s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTA 704s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTA 704s Processing line... 704s Processing line... 704s CGGACTGGTGACGCCGTTGAACGTGCGGCG 704s CGGNCTGGTGACGCCGTTGAACGTGCGGCG 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s ATCGCGCGGTTGTTTGGTGTGGACGGGGGTCTCAGGTT 704s ATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTT 704s Processing line... 704s Processing line... 704s Processing line... 704s AGGCCGTTGGGGTTCGCCGT 704s AGGCCGTTGGGGTTCGCCGT 704s Processing line... 704s CGTTCCCGGTGTGTCGTTGTAGGCC 704s CGTTCCCGGTGTGTCGTTGTAGGCC 704s Processing line... 704s CGTTCCCGGTGTGTCGTTGTAGGCC 704s CGTTCCCGGTGTGTCGTTGTAGGCC 704s Processing line... 704s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCG 704s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCG 704s Processing line... 704s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCG 704s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCG 704s Processing line... 704s Processing line... 704s Processing line... 704s TTTATGTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGGTTGGAGTCCGGCGGCCCGTTCGGTAGCGG 704s TTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGC-G 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s GTGCGGCGGGGCCAGTTCGAT 704s GTGCGGCGGGGCCAGTTCGAT 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s GGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATTTCATCGCGCGGTTGTTTGGTGTGGACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCTTTAGGTAGCG 704s GGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCG 704s Processing line... 704s GGCCCTTTAGGTAGCGGACTGGTGACGCCGTTGAACGTGCGG 704s GGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCGG 704s Processing line... 704s Processing line... 704s Processing line... 704s GGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTC-----T 704s GGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGT 704s --- Summary --- 704s Read 1 reference strings 704s Checked 28 alignments, 0 edits 704s --------------- 704s PASSED 704s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 704s /usr/bin/bowtie2 -D 20 --gbar 2 --score-min L,7.71077271151155,1.36210382207242 --mm --cp-min 4 --np 2 --large-index --mp 5.51213249309513,2.78592040287481 --trim3 9 -a --cp-ival 1 --local --qseq -p 3 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 704s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (1) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 704s 103 reads; of these: 704s 103 (100.00%) were unpaired; of these: 704s 80 (77.67%) aligned 0 times 704s 18 (17.48%) aligned exactly 1 time 704s 5 (4.85%) aligned >1 times 704s 22.33% overall alignment rate 704s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 704s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 704s Flattened IUPAC characters 704s Mutating sequence Sim.pm.1 704s Introducing 6 SNPs, 3/2 ref/read gaps, and 2 rearrangements 704s Finished SNPs 704s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 704s Finished ref gaps 704s Finished read gaps 704s Mutating sequence Sim.pm.2 704s Introducing 12 SNPs, 0/1 ref/read gaps, and 5 rearrangements 704s Finished SNPs 704s Finished ref gaps 704s Finished read gaps 704s Mutated reference genome to subject genome 704s SNPs introduced: 18 704s Reference gaps introduced: 3 704s Read gaps introduced: 3 704s Rearrangements introduced: 7 704s Created read sampler 704s Sampling 66 reads 704s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 704s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 704s parsing sequence Sim.pm.1... 704s parsing sequence Sim.pm.2... 704s Parsed 234 reference bases 704s *** Run 83 of 100 704s /usr/bin/bowtie2 --rfg 16.0657008106748,18.3991147311985 --nofw --cp-ival 2 -a --trim5 8 --n-ceil 0.119598858135707,1.12153026965916 --rdg 34.4250252056528,6.6141497172428 --score-min L,8.07375190186729,7.76279840703954 -D 7 --gbar 1 -R 3 --large-index --cp-min 7 -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 704s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 704s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '3' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 704s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '10' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 704s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '13' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 704s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '17' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 704s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '18' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 704s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 704s Warning: skipping read '25' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 704s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '42' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 704s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '43' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 704s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '44' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 704s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '46' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 704s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '51' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 704s 66 reads; of these: 704s 66 (100.00%) were unpaired; of these: 704s 59 (89.39%) aligned 0 times 704s 4 (6.06%) aligned exactly 1 time 704s 3 (4.55%) aligned >1 times 704s 10.61% overall alignment rate 704s Read 50 alignments... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s AA 704s AA 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s GGTC 704s GGTC 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s AGGCCGTTGGG 704s AGGCCGTTGGG 704s Processing line... 704s AGGCCGTTGGG 704s AGGCCGTTGGG 704s Processing line... 704s TTTATGTCATCGCGCGGTTG 704s TTTATGTCATCGCGCGGTTG 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s TGTAGG 704s TGTAGG 704s Processing line... 704s TGTAGG 704s TGTAGG 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s TGTCGTTGTAGGCCGTTGGG 704s TGTCGTTGTAGGCCGTTGGG 704s Processing line... 704s TGTCGTTGTAGGCCGTTGGG 704s TGTCGTTGTAGGCCGTTGGG 704s Processing line... 704s Processing line... 704s TTCGGTTGGTTTATGTCATCGCG 704s TTCGGTTGGTTTATGTCATCGCG 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s --- Summary --- 704s Read 1 reference strings 704s Checked 10 alignments, 0 edits 704s --------------- 704s PASSED 704s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 704s /usr/bin/bowtie2 --rfg 16.0657008106748,18.3991147311985 --nofw --cp-ival 2 -a --trim5 8 --n-ceil 0.119598858135707,1.12153026965916 --rdg 34.4250252056528,6.6141497172428 --score-min L,8.07375190186729,7.76279840703954 -D 7 --gbar 1 -R 3 --large-index --cp-min 7 -q -p 2 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 704s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 704s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '3' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 704s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '10' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 704s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '13' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 704s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '17' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 704s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '18' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 704s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 704s Warning: skipping read '25' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 704s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '42' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 704s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '43' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 704s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '44' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 704s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '46' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 704s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 704s Warning: skipping read '51' because it was < 2 characters long 704s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 704s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 704s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 704s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 704s 66 reads; of these: 704s 66 (100.00%) were unpaired; of these: 704s 59 (89.39%) aligned 0 times 704s 4 (6.06%) aligned exactly 1 time 704s 3 (4.55%) aligned >1 times 704s 10.61% overall alignment rate 704s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 704s Flattened IUPAC characters 704s Mutating sequence Sim.pm.2 704s Introducing 13 SNPs, 0/0 ref/read gaps, and 0 rearrangements 704s Finished SNPs 704s Finished ref gaps 704s Finished read gaps 704s Mutating sequence Sim.pm.1 704s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 704s Finished SNPs 704s Finished ref gaps 704s Finished read gaps 704s Mutated reference genome to subject genome 704s SNPs introduced: 18 704s Reference gaps introduced: 0 704s Read gaps introduced: 0 704s *** Run 84 of 100 704s /usr/bin/bowtie2 --mp 3.8212886125825,1.85712981450187 --trim3 7 --norc --n-ceil 0.252866063962511,1.0101019667269 --trim5 1 --cp-ival 1 --local -D 20 --gbar 1 --score-min L,6.99573255220301,5.63886956465613 --rdg 17.4479798968315 --np 1 --cp-min 5 --large-index --qseq -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq 704s Rearrangements introduced: 0 704s Created read sampler 704s Sampling 62 reads 704s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 704s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 704s parsing sequence Sim.pm.1... 704s parsing sequence Sim.pm.2... 704s Parsed 234 reference bases 704s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 704s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 704s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 704s 62 reads; of these: 704s 62 (100.00%) were unpaired; of these: 704s 62 (100.00%) aligned 0 times 704s 0 (0.00%) aligned exactly 1 time 704s 0 (0.00%) aligned >1 times 704s 0.00% overall alignment rate 704s Read 50 alignments... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s Processing line... 704s --- Summary --- 704s Read 1 reference strings 704s Checked 0 alignments, 0 edits 704s --------------- 704s PASSED 704s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 704s /usr/bin/bowtie2 --mp 3.8212886125825,1.85712981450187 --trim3 7 --norc --n-ceil 0.252866063962511,1.0101019667269 --trim5 1 --cp-ival 1 --local -D 20 --gbar 1 --score-min L,6.99573255220301,5.63886956465613 --rdg 17.4479798968315 --np 1 --cp-min 5 --large-index --qseq -p 3 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 705s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 705s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 705s 62 reads; of these: 705s 62 (100.00%) were unpaired; of these: 705s 62 (100.00%) aligned 0 times 705s 0 (0.00%) aligned exactly 1 time 705s 0 (0.00%) aligned >1 times 705s 0.00% overall alignment rate 705s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 705s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 705s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 705s Flattened IUPAC characters 705s Mutating sequence Sim.pm.2 705s Introducing 9 SNPs, 1/3 ref/read gaps, and 3 rearrangements 705s Finished SNPs 705s Finished ref gaps 705s Finished read gaps 705s Mutating sequence Sim.pm.1 705s Introducing 10 SNPs, 1/2 ref/read gaps, and 1 rearrangements 705s Finished SNPs 705s Finished ref gaps 705s Finished read gaps 705s Mutated reference genome to subject genome 705s SNPs introduced: 19 705s Reference gaps introduced: 2 705s Read gaps introduced: 5 705s Rearrangements introduced: 4 705s Created read sampler 705s Sampling 81 reads 705s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 705s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 705s parsing sequence Sim.pm.1... 705s parsing sequence Sim.pm.2... 705s Parsed 234 reference bases 705s *** Run 85 of 100 705s /usr/bin/bowtie2 --mm --rfg 44.6633910124135,1.30252429689959 --gbar 3 --score-min L,2.84409346606021,6.01218941297201 --ma 1.83769315956343 --cp-ival 1 --trim5 0 --large-index --cp-min 3 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 705s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 705s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '5' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 705s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #2 of read '6' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 705s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '8' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 705s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #2 of read '25' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 705s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '41' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 705s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '64' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 705s Read 50 alignments... 705s Read 100 alignments... 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 705s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '67' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 705s 81 reads; of these: 705s 81 (100.00%) were paired; of these: 705s 78 (96.30%) aligned concordantly 0 times 705s 1 (1.23%) aligned concordantly exactly 1 time 705s 2 (2.47%) aligned concordantly >1 times 705s ---- 705s 78 pairs aligned concordantly 0 times; of these: 705s 0 (0.00%) aligned discordantly 1 time 705s ---- 705s 78 pairs aligned 0 times concordantly or discordantly; of these: 705s 156 mates make up the pairs; of these: 705s 129 (82.69%) aligned 0 times 705s 9 (5.77%) aligned exactly 1 time 705s 18 (11.54%) aligned >1 times 705s 20.37% overall alignment rate 705s Read 150 alignments... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GCGGCC 705s GCGGCC 705s Processing line... 705s Processing line... 705s CCGGTGTGTCGTT 705s CCGGTGTGTCGTT 705s Processing line... 705s Processing line... 705s GGTG 705s GGTG 705s Processing line... 705s Processing line... 705s CC 705s CC 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GTTGGAG 705s GTTGGAG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GGTGC 705s GGTGC 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GTTCC 705s GTTCC 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GGTTC 705s GGTTC 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s CGTTC 705s CGTTC 705s Processing line... 705s Processing line... 705s TTG 705s TTG 705s Processing line... 705s GTTCGCCG 705s GTTCGCCG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GTGTCGTTGTAGGCCGTTGGGGTTCCC 705s GTGTCGTTGTAGGCCGTTGGGGTTCCC 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GTTGTAGGCCG 705s GTTGTAGGCCG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GTTGG 705s GTTGG 705s Processing line... 705s Processing line... 705s TTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 705s TTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 705s Processing line... 705s Processing line... 705s CGGCG 705s CGGCG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GG 705s GG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GGTGTGTCGTTGT 705s GGTGTGTCGTTGT 705s Processing line... 705s Processing line... 705s CTCAGGTTGGAGTCCC 705s CTCAGGTTGGAGTCCC 705s Processing line... 705s GCCCG 705s GCCCG 705s Processing line... 705s GCGGCGGGGCCAGTTCGAT 705s GCGGCGGGGCCAGTTCGAT 705s Processing line... 705s Processing line... 705s GTTT 705s GTTT 705s Processing line... 705s Processing line... 705s CCGTT 705s CCGTT 705s Processing line... 705s Processing line... 705s TGGA 705s TGGA 705s Processing line... 705s TTGGGGTTCGCCGTTCCCGGTGT 705s TTGGGGTTCGCCGTTCCCGGTGT 705s Processing line... 705s TAGGCCGTTGG 705s TAGGCCGTTGG 705s Processing line... 705s Processing line... 705s AGGCCGTTGGGGTTC 705s AGGCCGTTGGGGTTC 705s Processing line... 705s Processing line... 705s CGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATG 705s CGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s CCGTTCCCGGT 705s CCGTTCCCGGT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s TTT 705s TTT 705s Processing line... 705s GTCATCGCGCGGT 705s GTCATCGCGCGGT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GTCTCAGGTTGGAGTCCCGCG 705s GTCTCAGGTTGGAGTCCCGCG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s CGGTTGGTTTATGT 705s CGGTTGGTTTATGT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s --- Summary --- 705s Read 1 reference strings 705s Checked 33 alignments, 0 edits 705s --------------- 705s PASSED 705s Flattened IUPAC characters 705s Mutating sequence Sim.pm.1 705s Introducing 17 SNPs, 0/3 ref/read gaps, and 2 rearrangements 705s Finished SNPs 705s Finished ref gaps 705s Finished read gaps 705s Mutating sequence Sim.pm.2 705s Introducing 10 SNPs, 0/3 ref/read gaps, and 0 rearrangements 705s Finished SNPs 705s Finished ref gaps 705s Finished read gaps 705s Mutated reference genome to subject genome 705s SNPs introduced: 27 705s Reference gaps introduced: 0 705s Read gaps introduced: 6 705s Rearrangements introduced: 2 705s Created read sampler 705s Sampling 132 reads 705s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 705s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 705s parsing sequence Sim.pm.1... 705s parsing sequence Sim.pm.2... 705s Parsed 234 reference bases 705s *** Run 86 of 100 705s /usr/bin/bowtie2 --trim5 8 --large-index -M 2 --cp-min 5 --cp-ival 1 --mp 7.27778624957978,5.01638308372002 -R 3 --score-min L,2.18462989092504,2.79560274194285 --trim3 4 --ma 4.77381558659222 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 705s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 705s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 705s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '1' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 705s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '4' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 705s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '7' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 705s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '9' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 705s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '11' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 705s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '13' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 705s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '15' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 705s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '20' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 705s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '24' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 705s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '26' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 705s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '27' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 705s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '29' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 705s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '31' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 705s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '35' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 705s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '38' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 705s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '39' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 705s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '41' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 705s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '43' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 705s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '47' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 705s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '48' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 705s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '59' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 705s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '60' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 705s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '61' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 705s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 705s Warning: skipping read '68' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 705s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '71' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 705s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '72' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 705s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '73' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 705s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '84' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 705s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '87' because it was < 2 characters long 705s Read 50 alignments... 705s Read 100 alignments... 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 705s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '88' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 705s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '105' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 705s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '112' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 705s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '113' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 705s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '114' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 705s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '123' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 705s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '125' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 705s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '126' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 705s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '127' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 705s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '128' because it was < 2 characters long 705s Read 150 alignments... 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 705s Read 200 alignments... 705s 132 reads; of these: 705s 96 (72.73%) were paired; of these: 705s 96 (100.00%) aligned concordantly 0 times 705s 0 (0.00%) aligned concordantly exactly 1 time 705s 0 (0.00%) aligned concordantly >1 times 705s ---- 705s 96 pairs aligned concordantly 0 times; of these: 705s 0 (0.00%) aligned discordantly 1 time 705s ---- 705s 96 pairs aligned 0 times concordantly or discordantly; of these: 705s 192 mates make up the pairs; of these: 705s 156 (81.25%) aligned 0 times 705s 15 (7.81%) aligned exactly 1 time 705s 21 (10.94%) aligned >1 times 705s 36 (27.27%) were unpaired; of these: 705s 32 (88.89%) aligned 0 times 705s 1 (2.78%) aligned exactly 1 time 705s 3 (8.33%) aligned >1 times 705s 17.54% overall alignment rate 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GGTCTCAGGTTGGAGTCCCG 705s GGTCTCAGGTTGGAGTCCCG 705s Processing line... 705s Processing line... 705s GGG 705s GGG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s TCCCGGTGTGTCGTT 705s TCCCGGTGTGTCGTT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s TTGGT 705s TTGGT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GGG 705s GGG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s AACGT 705s AACGT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s TTTATGTCATCGCGCGGTTGTTTGG 705s TTTATGTCATCGCGCGGTTGTTTGG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GGCC 705s GGCC 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s CGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGC 705s CGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGC 705s Processing line... 705s Processing line... 705s TGG 705s TGG 705s Processing line... 705s Processing line... 705s AGGT 705s AGGT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTG 705s GCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s TT 705s TT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s CTCAGGTTGGAGTCCCGCGG 705s CTCAGGTTGGAGTCCCGCGG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GGTGTGTCG 705s GGTGTGTCG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s TTCCCGGTG 705s TTCCCGGTG 705s Processing line... 705s Processing line... 705s GTGTCGTT 705s GTGTCGTT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GGCGGG 705s GGCGGG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GGGCCAGTTCGATTCGG 705s GGGCCAGTTCGATTCGG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GTT 705s GTT 705s Processing line... 705s Processing line... 705s CGAT 705s CGAT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GCCGTTC 705s GCCGTTC 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GTGTCGTTGTAGGCCGTTGGG 705s GTGTCGTTGTAGGCCGTTGGG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GTCG 705s GTCG 705s Processing line... 705s Processing line... 705s Processing line... 705s GGGGGCGTGGGTGCGGCGG 705s GGGGGCGTGGGTGCGGCGG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s CGTGGGTGCGGCGGGGCC 705s CGTGGGTGCGGCGGGGCC 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGG 705s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGG 705s Processing line... 705s TGC 705s TGC 705s Processing line... 705s Processing line... 705s Processing line... 705s GTGTCGTT 705s GTGTCGTT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s TGCGGCGGGGCC 705s TGCGGCGGGGCC 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTG 705s GTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s AGGTTGGAGTCCCG 705s AGGTTGGAGTCCCG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GGGGTTCGCCGTTCCCGGT 705s GGGGTTCGCCGTTCCCGGT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GTCTCAGGTTGGAGTCCCGC 705s GTCTCAGGTTGGAGTCCCGC 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s CCAGTTCG 705s CCAGTTCG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s CGTTG 705s CGTTG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s CGGTGTG 705s CGGTGTG 705s Processing line... 705s Processing line... 705s ATCGCGCGGT 705s ATCGCGCGGT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s CCGGTGTGTC 705s CCGGTGTGTC 705s Processing line... 705s Processing line... 705s GAGTC 705s GAGTC 705s Processing line... 705s Processing line... 705s --- Summary --- 705s Read 1 reference strings 705s Checked 40 alignments, 0 edits 705s --------------- 705s PASSED 705s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 705s /usr/bin/bowtie2 --trim5 8 --large-index -M 2 --cp-min 5 --cp-ival 1 --mp 7.27778624957978,5.01638308372002 -R 3 --score-min L,2.18462989092504,2.79560274194285 --trim3 4 --ma 4.77381558659222 -r -p 4 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 705s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 705s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 705s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '1' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 705s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '4' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 705s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '7' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 705s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '9' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 705s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '11' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 705s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '13' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 705s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '15' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 705s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '20' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 705s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '24' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 705s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '26' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 705s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '27' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 705s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '29' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 705s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '31' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 705s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '35' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 705s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '38' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 705s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '39' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 705s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '41' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 705s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '43' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 705s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '47' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 705s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '48' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 705s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 705s Warning: skipping read '68' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 705s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '71' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 705s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '72' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 705s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '73' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 705s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '59' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 705s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '60' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 705s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '61' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 705s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '84' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 705s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '87' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 705s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '88' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 705s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '112' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 705s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '105' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 705s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '128' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 705s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '113' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 705s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '114' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 705s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '123' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 705s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '125' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 705s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '126' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 705s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '127' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 705s 132 reads; of these: 705s 96 (72.73%) were paired; of these: 705s 96 (100.00%) aligned concordantly 0 times 705s 0 (0.00%) aligned concordantly exactly 1 time 705s 0 (0.00%) aligned concordantly >1 times 705s ---- 705s 96 pairs aligned concordantly 0 times; of these: 705s 0 (0.00%) aligned discordantly 1 time 705s ---- 705s 96 pairs aligned 0 times concordantly or discordantly; of these: 705s 192 mates make up the pairs; of these: 705s 156 (81.25%) aligned 0 times 705s 15 (7.81%) aligned exactly 1 time 705s 21 (10.94%) aligned >1 times 705s 36 (27.27%) were unpaired; of these: 705s 32 (88.89%) aligned 0 times 705s 1 (2.78%) aligned exactly 1 time 705s 3 (8.33%) aligned >1 times 705s 17.54% overall alignment rate 705s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 705s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 705s Flattened IUPAC characters 705s Mutating sequence Sim.pm.2 705s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 705s Introducing 3 SNPs, 0/2 ref/read gaps, and 1 rearrangements 705s Finished SNPs 705s Finished ref gaps 705s Finished read gaps 705s Mutating sequence Sim.pm.1 705s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 705s Finished SNPs 705s Finished ref gaps 705s Finished read gaps 705s Mutated reference genome to subject genome 705s SNPs introduced: 11 705s Reference gaps introduced: 1 705s Read gaps introduced: 2 705s Rearrangements introduced: 1 705s Created read sampler 705s Sampling 99 reads 705s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 705s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 705s parsing sequence Sim.pm.1... 705s *** Run 87 of 100 705s /usr/bin/bowtie2 --local --cp-ival 3 --norc --trim3 5 --mp 5.47199451602974,3.11433421155364 -i S,2.87091707532664,5.43413103180991 --large-index --cp-min 4 --rdg 43.4734896576249,19.1056282068502 --mm --score-min L,4.51122314364368,5.37487715103876 -f -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fasta -2 /tmp/Sim.pm.RKKEKvBt_2.fasta 705s parsing sequence Sim.pm.2... 705s Parsed 234 reference bases 705s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '14' because it was < 2 characters long 705s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '15' because it was < 2 characters long 705s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '16' because it was < 2 characters long 705s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '25' because it was < 2 characters long 705s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '37' because it was < 2 characters long 705s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '39' because it was < 2 characters long 705s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #2 of read '41' because it was < 2 characters long 705s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '43' because it was < 2 characters long 705s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '50' because it was < 2 characters long 705s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '51' because it was < 2 characters long 705s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '54' because it was < 2 characters long 705s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '61' because it was < 2 characters long 705s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '64' because it was < 2 characters long 705s Read 50 alignments... 705s Read 100 alignments... 705s Warning: skipping mate #2 of read '67' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #2 of read '67' because it was < 2 characters long 705s Warning: skipping mate #2 of read '70' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #2 of read '70' because it was < 2 characters long 705s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '71' because it was < 2 characters long 705s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '89' because it was < 2 characters long 705s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read '93' because it was < 2 characters long 705s 99 reads; of these: 705s 89 (89.90%) were paired; of these: 705s 89 (100.00%) aligned concordantly 0 times 705s 0 (0.00%) aligned concordantly exactly 1 time 705s 0 (0.00%) aligned concordantly >1 times 705s ---- 705s 89 pairs aligned concordantly 0 times; of these: 705s 0 (0.00%) aligned discordantly 1 time 705s ---- 705s 89 pairs aligned 0 times concordantly or discordantly; of these: 705s 178 mates make up the pairs; of these: 705s 178 (100.00%) aligned 0 times 705s 0 (0.00%) aligned exactly 1 time 705s 0 (0.00%) aligned >1 times 705s 10 (10.10%) were unpaired; of these: 705s 10 (100.00%) aligned 0 times 705s 0 (0.00%) aligned exactly 1 time 705s 0 (0.00%) aligned >1 times 705s 0.00% overall alignment rate 705s Read 150 alignments... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s --- Summary --- 705s Read 1 reference strings 705s Checked 0 alignments, 0 edits 705s --------------- 705s PASSED 705s Flattened IUPAC characters 705s Mutating sequence Sim.pm.1 705s Introducing 2 SNPs, 1/2 ref/read gaps, and 0 rearrangements 705s Finished SNPs 705s Finished ref gaps 705s Finished read gaps 705s Mutating sequence Sim.pm.2 705s Introducing 9 SNPs, 0/0 ref/read gaps, and 3 rearrangements 705s Finished SNPs 705s Finished ref gaps 705s Finished read gaps 705s Mutated reference genome to subject genome 705s SNPs introduced: 11 705s Reference gaps introduced: 1 705s Read gaps introduced: 2 705s Rearrangements introduced: 3 705s Created read sampler 705s Sampling 17 reads 705s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.qseq & /tmp/Sim.pm.RKKEKvBt_2.qseq 705s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 705s parsing sequence Sim.pm.1... 705s parsing sequence Sim.pm.2... 705s Parsed 234 reference bases 705s *** Run 88 of 100 705s /usr/bin/bowtie2 --score-min L,2.72269212986754,3.96445300382492 --rfg 47.7272082910932,12.5992505675816 --mm --large-index --cp-min 10 --np 1 --norc --cp-ival 3 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 705s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 705s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 705s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 705s 17 reads; of these: 705s 17 (100.00%) were paired; of these: 705s 17 (100.00%) aligned concordantly 0 times 705s 0 (0.00%) aligned concordantly exactly 1 time 705s 0 (0.00%) aligned concordantly >1 times 705s ---- 705s 17 pairs aligned concordantly 0 times; of these: 705s 0 (0.00%) aligned discordantly 1 time 705s ---- 705s 17 pairs aligned 0 times concordantly or discordantly; of these: 705s 34 mates make up the pairs; of these: 705s 28 (82.35%) aligned 0 times 705s 1 (2.94%) aligned exactly 1 time 705s 5 (14.71%) aligned >1 times 705s 17.65% overall alignment rate 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s AC 705s AC 705s Processing line... 705s Processing line... 705s GA 705s GA 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s CA 705s CA 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GTTTATGTCATCGCGCGGTTGTTTGGT 705s GTTTATGTCATCGCGCGGTTGTTTGGT 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s GGCCG 705s GGCCG 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s ACG 705s ACG 705s Processing line... 705s Processing line... 705s Processing line... 705s --- Summary --- 705s Read 1 reference strings 705s Checked 6 alignments, 0 edits 705s --------------- 705s PASSED 705s ALSO checking that bowtie2 and bowtie2-align match up 705s /usr/bin/bowtie2 --score-min L,2.72269212986754,3.96445300382492 --rfg 47.7272082910932,12.5992505675816 --mm --large-index --cp-min 10 --np 1 --norc --cp-ival 3 --qseq -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.qseq -2 /tmp/Sim.pm.RKKEKvBt_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 705s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 705s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 705s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 705s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 705s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 705s 17 reads; of these: 705s 17 (100.00%) were paired; of these: 705s 17 (100.00%) aligned concordantly 0 times 705s 0 (0.00%) aligned concordantly exactly 1 time 705s 0 (0.00%) aligned concordantly >1 times 705s ---- 705s 17 pairs aligned concordantly 0 times; of these: 705s 0 (0.00%) aligned discordantly 1 time 705s ---- 705s 17 pairs aligned 0 times concordantly or discordantly; of these: 705s 34 mates make up the pairs; of these: 705s 28 (82.35%) aligned 0 times 705s 1 (2.94%) aligned exactly 1 time 705s 5 (14.71%) aligned >1 times 705s 17.65% overall alignment rate 705s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 705s Flattened IUPAC characters 705s Mutating sequence Sim.pm.2 705s Introducing 12 SNPs, 1/1 ref/read gaps, and 0 rearrangements 705s Finished SNPs 705s Finished ref gaps 705s Finished read gaps 705s Mutating sequence Sim.pm.1 705s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 705s Finished SNPs 705s Finished ref gaps 705s Finished read gaps 705s Mutated reference genome to subject genome 705s SNPs introduced: 13 705s Reference gaps introduced: 1 705s Read gaps introduced: 1 705s Rearrangements introduced: 1 705s Created read sampler 705s Sampling 30 reads 705s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 705s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 705s parsing sequence Sim.pm.1... 705s parsing sequence Sim.pm.2... 705s Parsed 234 reference bases 705s *** Run 89 of 100 705s /usr/bin/bowtie2 --large-index --np 2 --cp-min 2 --rdg 10.9958725453583 -k 3 --score-min L,7.77643426367869,4.74412366154162 --cp-ival 3 --local --trim5 1 --rfg 25.5342452155477 -i L,0.453449419254065 --mp 2.5383732084938,1.78647792006406 --trim3 6 -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw 705s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '1' because it was < 2 characters long 705s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '2' because it was < 2 characters long 705s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '3' because it was < 2 characters long 705s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '14' because it was < 2 characters long 705s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '15' because it was < 2 characters long 705s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '17' because it was < 2 characters long 705s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '18' because it was < 2 characters long 705s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 705s Warning: skipping read '21' because it was < 2 characters long 705s 30 reads; of these: 705s 30 (100.00%) were unpaired; of these: 705s 30 (100.00%) aligned 0 times 705s 0 (0.00%) aligned exactly 1 time 705s 0 (0.00%) aligned >1 times 705s 0.00% overall alignment rate 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s Processing line... 705s --- Summary --- 705s Read 1 reference strings 705s Checked 0 alignments, 0 edits 705s --------------- 705s PASSED 705s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 705s /usr/bin/bowtie2 --large-index --np 2 --cp-min 2 --rdg 10.9958725453583 -k 3 --score-min L,7.77643426367869,4.74412366154162 --cp-ival 3 --local --trim5 1 --rfg 25.5342452155477 -i L,0.453449419254065 --mp 2.5383732084938,1.78647792006406 --trim3 6 -r -p 4 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 706s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 706s Warning: skipping read '1' because it was < 2 characters long 706s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 706s Warning: skipping read '2' because it was < 2 characters long 706s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 706s Warning: skipping read '3' because it was < 2 characters long 706s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 706s Warning: skipping read '14' because it was < 2 characters long 706s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 706s Warning: skipping read '15' because it was < 2 characters long 706s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 706s Warning: skipping read '17' because it was < 2 characters long 706s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 706s Warning: skipping read '18' because it was < 2 characters long 706s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 706s Warning: skipping read '21' because it was < 2 characters long 706s 30 reads; of these: 706s 30 (100.00%) were unpaired; of these: 706s 30 (100.00%) aligned 0 times 706s 0 (0.00%) aligned exactly 1 time 706s 0 (0.00%) aligned >1 times 706s 0.00% overall alignment rate 706s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 706s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 706s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 706s Flattened IUPAC characters 706s Mutating sequence Sim.pm.1 706s Introducing 19 SNPs, 3/0 ref/read gaps, and 0 rearrangements 706s Finished SNPs 706s Finished ref gaps 706s Finished read gaps 706s Mutating sequence Sim.pm.2 706s Introducing 11 SNPs, 1/3 ref/read gaps, and 0 rearrangements 706s Finished SNPs 706s Finished ref gaps 706s Finished read gaps 706s Mutated reference genome to subject genome 706s SNPs introduced: 30 706s Reference gaps introduced: 4 706s Read gaps introduced: 3 706s Rearrangements introduced: 0 706s Created read sampler 706s Sampling 96 reads 706s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 706s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 706s parsing sequence Sim.pm.1... 706s parsing sequence Sim.pm.2... 706s Parsed 234 reference bases 706s *** Run 90 of 100 706s /usr/bin/bowtie2 --large-index --cp-min 2 --rdg 19.2075757666696 --mm --score-min L,4.68593266527368,7.69099886656502 -k 3 -D 26 --gbar 26 --local --cp-ival 3 --nofw --trim3 3 -N 0 -L20 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 706s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 706s Warning: skipping mate #1 of read '9' because it was < 2 characters long 706s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 706s Warning: skipping mate #1 of read '11' because it was < 2 characters long 706s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 706s Warning: skipping mate #1 of read '13' because it was < 2 characters long 706s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #1 of read '38' because it was < 2 characters long 706s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #2 of read '40' because it was < 2 characters long 706s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 706s Warning: skipping read '42' because it was < 2 characters long 706s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #1 of read '67' because it was < 2 characters long 706s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #2 of read '82' because it was < 2 characters long 706s Read 50 alignments... 706s Read 100 alignments... 706s 96 reads; of these: 706s 87 (90.62%) were paired; of these: 706s 87 (100.00%) aligned concordantly 0 times 706s 0 (0.00%) aligned concordantly exactly 1 time 706s 0 (0.00%) aligned concordantly >1 times 706s ---- 706s 87 pairs aligned concordantly 0 times; of these: 706s 0 (0.00%) aligned discordantly 1 time 706s ---- 706s 87 pairs aligned 0 times concordantly or discordantly; of these: 706s 174 mates make up the pairs; of these: 706s 174 (100.00%) aligned 0 times 706s 0 (0.00%) aligned exactly 1 time 706s 0 (0.00%) aligned >1 times 706s 9 (9.38%) were unpaired; of these: 706s 9 (100.00%) aligned 0 times 706s 0 (0.00%) aligned exactly 1 time 706s 0 (0.00%) aligned >1 times 706s 0.00% overall alignment rate 706s Read 150 alignments... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s --- Summary --- 706s Read 1 reference strings 706s Checked 0 alignments, 0 edits 706s --------------- 706s PASSED 706s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 706s /usr/bin/bowtie2 --large-index --cp-min 2 --rdg 19.2075757666696 --mm --score-min L,4.68593266527368,7.69099886656502 -k 3 -D 26 --gbar 26 --local --cp-ival 3 --nofw --trim3 3 -N 0 -L20 -q -p 4 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 706s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 706s Warning: skipping mate #1 of read '9' because it was < 2 characters long 706s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 706s Warning: skipping mate #1 of read '11' because it was < 2 characters long 706s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 706s Warning: skipping mate #1 of read '13' because it was < 2 characters long 706s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #1 of read '38' because it was < 2 characters long 706s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #2 of read '40' because it was < 2 characters long 706s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 706s Warning: skipping read '42' because it was < 2 characters long 706s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #1 of read '67' because it was < 2 characters long 706s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #2 of read '82' because it was < 2 characters long 706s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 706s 96 reads; of these: 706s 87 (90.62%) were paired; of these: 706s 87 (100.00%) aligned concordantly 0 times 706s 0 (0.00%) aligned concordantly exactly 1 time 706s 0 (0.00%) aligned concordantly >1 times 706s ---- 706s 87 pairs aligned concordantly 0 times; of these: 706s 0 (0.00%) aligned discordantly 1 time 706s ---- 706s 87 pairs aligned 0 times concordantly or discordantly; of these: 706s 174 mates make up the pairs; of these: 706s 174 (100.00%) aligned 0 times 706s 0 (0.00%) aligned exactly 1 time 706s 0 (0.00%) aligned >1 times 706s 9 (9.38%) were unpaired; of these: 706s 9 (100.00%) aligned 0 times 706s 0 (0.00%) aligned exactly 1 time 706s 0 (0.00%) aligned >1 times 706s 0.00% overall alignment rate 706s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 706s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 706s Flattened IUPAC characters 706s Mutating sequence Sim.pm.1 706s Introducing 1 SNPs, 1/0 ref/read gaps, and 1 rearrangements 706s Finished SNPs 706s Finished ref gaps 706s Finished read gaps 706s Mutating sequence Sim.pm.2 706s Introducing 16 SNPs, 1/0 ref/read gaps, and 0 rearrangements 706s Finished SNPs 706s Finished ref gaps 706s Finished read gaps 706s Mutated reference genome to subject genome 706s SNPs introduced: 17 706s Reference gaps introduced: 2 706s Read gaps introduced: 0 706s Rearrangements introduced: 1 706s Created read sampler 706s Sampling 65 reads 706s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 706s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 706s *** Run 91 of 100 706s /usr/bin/bowtie2 --score-min L,2.29861283599496,9.5274082812619 --rdg 29.2751611766353,1.5449992159032 --cp-min 3 --large-index --nofw --mp 6.48941713320113,3.44591693296234 -N 1 -L30 -M 4 --trim5 0 --norc --local --cp-ival 1 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 706s parsing sequence Sim.pm.1... 706s parsing sequence Sim.pm.2... 706s Parsed 234 reference bases 706s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 706s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (1) 706s Warning: skipping mate #2 of read '34' because it was < 2 characters long 706s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (1) 706s Warning: skipping mate #1 of read '46' because it was < 2 characters long 706s Read 50 alignments... 706s Read 100 alignments... 706s 65 reads; of these: 706s 65 (100.00%) were paired; of these: 706s 65 (100.00%) aligned concordantly 0 times 706s 0 (0.00%) aligned concordantly exactly 1 time 706s 0 (0.00%) aligned concordantly >1 times 706s ---- 706s 65 pairs aligned concordantly 0 times; of these: 706s 0 (0.00%) aligned discordantly 1 time 706s ---- 706s 65 pairs aligned 0 times concordantly or discordantly; of these: 706s 130 mates make up the pairs; of these: 706s 130 (100.00%) aligned 0 times 706s 0 (0.00%) aligned exactly 1 time 706s 0 (0.00%) aligned >1 times 706s 0.00% overall alignment rate 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s /usr/bin/bowtie2 --score-min L,2.29861283599496,9.5274082812619 --rdg 29.2751611766353,1.5449992159032 --cp-min 3 --large-index --nofw --mp 6.48941713320113,3.44591693296234 -N 1 -L30 -M 4 --trim5 0 --norc --local --cp-ival 1 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s --- Summary --- 706s Read 1 reference strings 706s Checked 0 alignments, 0 edits 706s --------------- 706s PASSED 706s ALSO checking that bowtie2 and bowtie2-align match up 706s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 706s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (1) 706s Warning: skipping mate #2 of read '34' because it was < 2 characters long 706s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (1) 706s Warning: skipping mate #1 of read '46' because it was < 2 characters long 706s 65 reads; of these: 706s 65 (100.00%) were paired; of these: 706s 65 (100.00%) aligned concordantly 0 times 706s 0 (0.00%) aligned concordantly exactly 1 time 706s 0 (0.00%) aligned concordantly >1 times 706s ---- 706s 65 pairs aligned concordantly 0 times; of these: 706s 0 (0.00%) aligned discordantly 1 time 706s ---- 706s 65 pairs aligned 0 times concordantly or discordantly; of these: 706s 130 mates make up the pairs; of these: 706s 130 (100.00%) aligned 0 times 706s 0 (0.00%) aligned exactly 1 time 706s 0 (0.00%) aligned >1 times 706s 0.00% overall alignment rate 706s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 706s Flattened IUPAC characters 706s Mutating sequence Sim.pm.1 706s Introducing 10 SNPs, 1/2 ref/read gaps, and 0 rearrangements 706s Finished SNPs 706s Finished ref gaps 706s Finished read gaps 706s Mutating sequence Sim.pm.2 706s Introducing 5 SNPs, 0/2 ref/read gaps, and 1 rearrangements 706s Finished SNPs 706s Finished ref gaps 706s Finished read gaps 706s Mutated reference genome to subject genome 706s SNPs introduced: 15 706s Reference gaps introduced: 1 706s Read gaps introduced: 4 706s Rearrangements introduced: 1 706s Created read sampler 706s Sampling 85 reads 706s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 706s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 706s parsing sequence Sim.pm.1... 706s parsing sequence Sim.pm.2... 706s Parsed 234 reference bases 706s *** Run 92 of 100 706s /usr/bin/bowtie2 --mp 2.90682523701347,1.50794875024615 -D 19 --gbar 1 --ma 2.55217049221252 --score-min L,6.27149211386071,6.54154033541257 --n-ceil 0.292449001156802,0.771686859705198 --cp-min 11 -M 4 --large-index --cp-ival 3 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 706s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 706s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 706s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #2 of read '32' because it was < 2 characters long 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 706s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #2 of read '44' because it was < 2 characters long 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 706s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #2 of read '45' because it was < 2 characters long 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 706s Read 50 alignments... 706s 85 reads; of these: 706s 85 (100.00%) were paired; of these: 706s 84 (98.82%) aligned concordantly 0 times 706s 0 (0.00%) aligned concordantly exactly 1 time 706s 1 (1.18%) aligned concordantly >1 times 706s ---- 706s 84 pairs aligned concordantly 0 times; of these: 706s 2 (2.38%) aligned discordantly 1 time 706s ---- 706s 82 pairs aligned 0 times concordantly or discordantly; of these: 706s 164 mates make up the pairs; of these: 706s 128 (78.05%) aligned 0 times 706s 21 (12.80%) aligned exactly 1 time 706s 15 (9.15%) aligned >1 times 706s 24.71% overall alignment rate 706s Read 100 alignments... 706s Read 150 alignments... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s GACGCCGTTGAACGTG 706s GACGCCGTTGAACGTG 706s Processing line... 706s Processing line... 706s CTCAGGTTGG 706s CTCAGGTTGG 706s Processing line... 706s Processing line... 706s CCGGTGT 706s CCGGTGT 706s Processing line... 706s CT 706s CT 706s Processing line... 706s GTGTGTCGTTGTAGGCCG 706s GTGTGTCGTTGTAGGCCG 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s CGTG 706s CGTG 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s ACGC 706s ACGC 706s Processing line... 706s Processing line... 706s GGGGCGTGGGTGCGGCGGGGCCAG 706s GGGGCGTGGGTGCGGCGGGGCCAG 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s TAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCG 706s TAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCG 706s Processing line... 706s Processing line... 706s ATCGCGCGG 706s ATCGCGCGG 706s Processing line... 706s Processing line... 706s GAACGTGCGGCGGG 706s GAACGTGCGGCGGG 706s Processing line... 706s Processing line... 706s GA 706s GA 706s Processing line... 706s Processing line... 706s GTGTGTCGTTGTAGGCCGTTGGGGTTC 706s GTGTGTCGTTGTAGGCCGTTGGGGTTC 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s GGTCTCAGGTTGGAGTCC 706s GGTCTCAGGTTGGAGTCC 706s Processing line... 706s Processing line... 706s GCGGTTGTTTGGT 706s GCGGTTGTTTGGT 706s Processing line... 706s Processing line... 706s CCAGTTCGATTCGGTTGGTTTA 706s CCAGTTCGATTCGGTTGGTTTA 706s Processing line... 706s Processing line... 706s GCC 706s GCC 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s AGCGG 706s AGCGG 706s Processing line... 706s Processing line... 706s TCGCGCGGTTGTTTGGTGT 706s TCGCGCGGTTGTTTGGTGT 706s Processing line... 706s Processing line... 706s TTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTT 706s TTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTT 706s Processing line... 706s TCT 706s TCT 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s GGCGTGGGTGCGGCGGG 706s GGCGTGGGTGCGGCGGG 706s Processing line... 706s Processing line... 706s CGC 706s CGC 706s Processing line... 706s Processing line... 706s GGTGCGGCGGGGCCAGTTCGATTCGGTTG 706s GGTGCGGCGGGGCCAGTTCGATTCGGTTG 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s GTAGGCCGTTGGGGTTCGCCG 706s GTAGGCCGTTGGGGTTCGCCG 706s Processing line... 706s Processing line... 706s GCCAGTTCGATTC 706s GCCAGTTCGATTC 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s GGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCCC 706s GGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCCC 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s ATTCGG 706s ATTCGG 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s GCCGTTGGGG 706s GCCGTTGGGG 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s CGATTCGG 706s CGATTCGG 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s AGGCCGTTGGGG 706s AGGCCGTTGGGG 706s Processing line... 706s Processing line... 706s GGTGCGGCG 706s GGTGCGGCG 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s CGTTGTA 706s CGTTGTA 706s Processing line... 706s TGG 706s TGG 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s AGTTCGAT 706s AGTTCGAT 706s Processing line... 706s Processing line... 706s GT 706s GT 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s Processing line... 706s TTGG 706s TTGG 706s Processing line... 706s Processing line... 706s GTTGAACGTGCGGCG 706s GTTGAACGTGCGGCG 706s Processing line... 706s Processing line... 706s CGGTGTGTCGTTGTAGGCC 706s CGGTGTGTCGTTGTAGGCC 706s Processing line... 706s GTTC 706s GTTC 706s Processing line... 706s GGGGTCTC 706s GGGGTCTC 706s Processing line... 706s AGC 706s AGC 706s Processing line... 706s Processing line... 706s --- Summary --- 706s Read 1 reference strings 706s Checked 42 alignments, 0 edits 706s --------------- 706s PASSED 706s ALSO checking that bowtie2 and bowtie2-align match up 706s /usr/bin/bowtie2 --mp 2.90682523701347,1.50794875024615 -D 19 --gbar 1 --ma 2.55217049221252 --score-min L,6.27149211386071,6.54154033541257 --n-ceil 0.292449001156802,0.771686859705198 --cp-min 11 -M 4 --large-index --cp-ival 3 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 706s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 706s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 706s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #2 of read '32' because it was < 2 characters long 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 706s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #2 of read '44' because it was < 2 characters long 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 706s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 706s Warning: skipping mate #2 of read '45' because it was < 2 characters long 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 706s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 707s 85 reads; of these: 707s 85 (100.00%) were paired; of these: 707s 84 (98.82%) aligned concordantly 0 times 707s 0 (0.00%) aligned concordantly exactly 1 time 707s 1 (1.18%) aligned concordantly >1 times 707s ---- 707s 84 pairs aligned concordantly 0 times; of these: 707s 2 (2.38%) aligned discordantly 1 time 707s ---- 707s 82 pairs aligned 0 times concordantly or discordantly; of these: 707s 164 mates make up the pairs; of these: 707s 128 (78.05%) aligned 0 times 707s 21 (12.80%) aligned exactly 1 time 707s 15 (9.15%) aligned >1 times 707s 24.71% overall alignment rate 707s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 707s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 707s /usr/bin/bowtie2 --mp 2.90682523701347,1.50794875024615 -D 19 --gbar 1 --ma 2.55217049221252 --score-min L,6.27149211386071,6.54154033541257 --n-ceil 0.292449001156802,0.771686859705198 --cp-min 11 -M 4 --large-index --cp-ival 3 -q -p 2 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 707s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 707s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 707s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '44' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 707s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '45' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 707s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '32' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 707s 85 reads; of these: 707s 85 (100.00%) were paired; of these: 707s 84 (98.82%) aligned concordantly 0 times 707s 0 (0.00%) aligned concordantly exactly 1 time 707s 1 (1.18%) aligned concordantly >1 times 707s ---- 707s 84 pairs aligned concordantly 0 times; of these: 707s 2 (2.38%) aligned discordantly 1 time 707s ---- 707s 82 pairs aligned 0 times concordantly or discordantly; of these: 707s 164 mates make up the pairs; of these: 707s 128 (78.05%) aligned 0 times 707s 21 (12.80%) aligned exactly 1 time 707s 15 (9.15%) aligned >1 times 707s 24.71% overall alignment rate 707s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 707s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 707s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 707s /usr/bin/bowtie2 --mp 2.90682523701347,1.50794875024615 -D 19 --gbar 1 --ma 2.55217049221252 --score-min L,6.27149211386071,6.54154033541257 --n-ceil 0.292449001156802,0.771686859705198 --cp-min 11 -M 4 --large-index --cp-ival 3 -q -p 3 -x /tmp/Sim.pm.RKKEKvBt --reorder -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 707s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 707s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 707s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 707s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '32' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 707s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '44' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 707s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '45' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 707s 85 reads; of these: 707s 85 (100.00%) were paired; of these: 707s 84 (98.82%) aligned concordantly 0 times 707s 0 (0.00%) aligned concordantly exactly 1 time 707s 1 (1.18%) aligned concordantly >1 times 707s ---- 707s 84 pairs aligned concordantly 0 times; of these: 707s 2 (2.38%) aligned discordantly 1 time 707s ---- 707s 82 pairs aligned 0 times concordantly or discordantly; of these: 707s 164 mates make up the pairs; of these: 707s 128 (78.05%) aligned 0 times 707s 21 (12.80%) aligned exactly 1 time 707s 15 (9.15%) aligned >1 times 707s 24.71% overall alignment rate 707s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 707s Flattened IUPAC characters 707s Mutating sequence Sim.pm.2 707s Introducing 3 SNPs, 0/0 ref/read gaps, and 3 rearrangements 707s Finished SNPs 707s Finished ref gaps 707s Finished read gaps 707s Mutating sequence Sim.pm.1 707s Introducing 10 SNPs, 0/0 ref/read gaps, and 2 rearrangements 707s Finished SNPs 707s Finished ref gaps 707s Finished read gaps 707s Mutated reference genome to subject genome 707s SNPs introduced: 13 707s Reference gaps introduced: 0 707s Read gaps introduced: 0 707s Rearrangements introduced: 5 707s Created read sampler 707s Sampling 78 reads 707s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 707s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 707s parsing sequence Sim.pm.1... 707s parsing sequence Sim.pm.2... 707s *** Run 93 of 100 707s /usr/bin/bowtie2 --large-index --cp-min 4 --np 1 -D 27 --score-min L,6.21969389062095,8.94147831994372 --rdg 20.5816111301244,2.99782122197319 -M 7 --cp-ival 1 --local --trim3 1 --rfg 28.4688157736554,18.1507098645951 -r -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw 707s Parsed 234 reference bases 707s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 707s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #1 of read '27' because it was < 2 characters long 707s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #1 of read '46' because it was < 2 characters long 707s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '49' because it was < 2 characters long 707s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '53' because it was < 2 characters long 707s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '62' because it was < 2 characters long 707s Read 50 alignments... 707s Read 100 alignments... 707s 78 reads; of these: 707s 75 (96.15%) were paired; of these: 707s 75 (100.00%) aligned concordantly 0 times 707s 0 (0.00%) aligned concordantly exactly 1 time 707s 0 (0.00%) aligned concordantly >1 times 707s ---- 707s 75 pairs aligned concordantly 0 times; of these: 707s 0 (0.00%) aligned discordantly 1 time 707s ---- 707s 75 pairs aligned 0 times concordantly or discordantly; of these: 707s 150 mates make up the pairs; of these: 707s 150 (100.00%) aligned 0 times 707s 0 (0.00%) aligned exactly 1 time 707s 0 (0.00%) aligned >1 times 707s 3 (3.85%) were unpaired; of these: 707s 3 (100.00%) aligned 0 times 707s 0 (0.00%) aligned exactly 1 time 707s 0 (0.00%) aligned >1 times 707s 0.00% overall alignment rate 707s Read 150 alignments... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s /usr/bin/bowtie2 --large-index --cp-min 4 --np 1 -D 27 --score-min L,6.21969389062095,8.94147831994372 --rdg 20.5816111301244,2.99782122197319 -M 7 --cp-ival 1 --local --trim3 1 --rfg 28.4688157736554,18.1507098645951 -r -p 2 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s --- Summary --- 707s Read 1 reference strings 707s Checked 0 alignments, 0 edits 707s --------------- 707s PASSED 707s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 707s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 707s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #1 of read '27' because it was < 2 characters long 707s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #1 of read '46' because it was < 2 characters long 707s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '49' because it was < 2 characters long 707s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '53' because it was < 2 characters long 707s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '62' because it was < 2 characters long 707s 78 reads; of these: 707s 75 (96.15%) were paired; of these: 707s 75 (100.00%) aligned concordantly 0 times 707s 0 (0.00%) aligned concordantly exactly 1 time 707s 0 (0.00%) aligned concordantly >1 times 707s ---- 707s 75 pairs aligned concordantly 0 times; of these: 707s 0 (0.00%) aligned discordantly 1 time 707s ---- 707s 75 pairs aligned 0 times concordantly or discordantly; of these: 707s 150 mates make up the pairs; of these: 707s 150 (100.00%) aligned 0 times 707s 0 (0.00%) aligned exactly 1 time 707s 0 (0.00%) aligned >1 times 707s 3 (3.85%) were unpaired; of these: 707s 3 (100.00%) aligned 0 times 707s 0 (0.00%) aligned exactly 1 time 707s 0 (0.00%) aligned >1 times 707s 0.00% overall alignment rate 707s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 707s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 707s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 707s /usr/bin/bowtie2 --large-index --cp-min 4 --np 1 -D 27 --score-min L,6.21969389062095,8.94147831994372 --rdg 20.5816111301244,2.99782122197319 -M 7 --cp-ival 1 --local --trim3 1 --rfg 28.4688157736554,18.1507098645951 -r -p 3 -x /tmp/Sim.pm.RKKEKvBt --reorder -1 /tmp/Sim.pm.RKKEKvBt_1.raw -2 /tmp/Sim.pm.RKKEKvBt_2.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 707s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 707s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 707s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #1 of read '27' because it was < 2 characters long 707s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #1 of read '46' because it was < 2 characters long 707s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '49' because it was < 2 characters long 707s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '53' because it was < 2 characters long 707s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (0) 707s Warning: skipping mate #2 of read '62' because it was < 2 characters long 707s 78 reads; of these: 707s 75 (96.15%) were paired; of these: 707s 75 (100.00%) aligned concordantly 0 times 707s 0 (0.00%) aligned concordantly exactly 1 time 707s 0 (0.00%) aligned concordantly >1 times 707s ---- 707s 75 pairs aligned concordantly 0 times; of these: 707s 0 (0.00%) aligned discordantly 1 time 707s ---- 707s 75 pairs aligned 0 times concordantly or discordantly; of these: 707s 150 mates make up the pairs; of these: 707s 150 (100.00%) aligned 0 times 707s 0 (0.00%) aligned exactly 1 time 707s 0 (0.00%) aligned >1 times 707s 3 (3.85%) were unpaired; of these: 707s 3 (100.00%) aligned 0 times 707s 0 (0.00%) aligned exactly 1 time 707s 0 (0.00%) aligned >1 times 707s 0.00% overall alignment rate 707s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 707s Flattened IUPAC characters 707s Mutating sequence Sim.pm.1 707s Introducing 11 SNPs, 0/2 ref/read gaps, and 2 rearrangements 707s Finished SNPs 707s Finished ref gaps 707s Finished read gaps 707s Mutating sequence Sim.pm.2 707s Introducing 9 SNPs, 1/1 ref/read gaps, and 1 rearrangements 707s Finished SNPs 707s Finished ref gaps 707s Finished read gaps 707s Mutated reference genome to subject genome 707s SNPs introduced: 20 707s Reference gaps introduced: 1 707s Read gaps introduced: 3 707s Rearrangements introduced: 3 707s Created read sampler 707s Sampling 130 reads 707s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 707s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 707s parsing sequence Sim.pm.1... 707s parsing sequence Sim.pm.2... 707s Parsed 234 reference bases 707s *** Run 94 of 100 707s /usr/bin/bowtie2 --n-ceil 0.104936212729466,1.02361175883887 --norc --np 1 --cp-min 3 -a --large-index --cp-ival 2 -N 1 -L14 --score-min L,2.91769022913821,8.62354453513459 --mm -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 707s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #1 of read '18' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 707s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #2 of read '41' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 707s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #2 of read '47' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 707s Read 50 alignments... 707s Read 100 alignments... 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 707s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #2 of read '72' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 707s Warning: skipping mate #1 of read '81' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #1 of read '81' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 707s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #1 of read '85' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 707s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #1 of read '96' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 707s Read 150 alignments... 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 707s Read 200 alignments... 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 707s Read 250 alignments... 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 707s Read 300 alignments... 707s Read 350 alignments... 707s 130 reads; of these: 707s 130 (100.00%) were paired; of these: 707s 126 (96.92%) aligned concordantly 0 times 707s 2 (1.54%) aligned concordantly exactly 1 time 707s 2 (1.54%) aligned concordantly >1 times 707s ---- 707s 126 pairs aligned concordantly 0 times; of these: 707s 0 (0.00%) aligned discordantly 1 time 707s ---- 707s 126 pairs aligned 0 times concordantly or discordantly; of these: 707s 252 mates make up the pairs; of these: 707s 222 (88.10%) aligned 0 times 707s 14 (5.56%) aligned exactly 1 time 707s 16 (6.35%) aligned >1 times 707s 14.62% overall alignment rate 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s TCGCCGTTCCCG 707s TCGCCGTTCCCG 707s Processing line... 707s TCGCCGTTCCCG 707s TCGCCGTTCCCG 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s GTGCGGCGGGGCCAGTTC 707s GTGCGGCGGGGCCAGTTC 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s CTCAGGTTGGAGTCCCGCGGC 707s CTCAGGTTGGAGTCCCGCGGC 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s GCCAGTTCGATTCG 707s GCCAGTTCGATTCG 707s Processing line... 707s Processing line... 707s GCCGTTCCCG 707s GCCGTTCCCG 707s Processing line... 707s GCCGTTCCCG 707s GCCGTTCCCG 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s CGGCGGGGCCAGTTCGA 707s CGGCGGGGCCAGTTCGA 707s Processing line... 707s GTCTCAGGTTGGAGTCCCGCGGCCCGTT 707s GTCTCAGGTTGGAGTCCCGCGGCCCGTT 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s TTCCCGGTGTGTCGTTGTAGGCCGTTGGGG 707s TTCCCGGTGTGTCGTTGTAGGCCGTTGGGG 707s Processing line... 707s TTCCCGGTGTGTCGTTGTAGGCCGTTGGGG 707s TTCCCGGTGTGTCGTTGTAGGCCGTTGGGG 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s GTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGT 707s GTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGT 707s Processing line... 707s Processing line... 707s TGG 707s TGG 707s Processing line... 707s TGG 707s TGG 707s Processing line... 707s TGG 707s TGG 707s Processing line... 707s TGG 707s TGG 707s Processing line... 707s TGG 707s TGG 707s Processing line... 707s TGG 707s TGG 707s Processing line... 707s TGG 707s TGG 707s Processing line... 707s TGG 707s TGG 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s CGA 707s CGA 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s AACG 707s AACG 707s Processing line... 707s Processing line... 707s GTTCC 707s GTTCC 707s Processing line... 707s GTTCC 707s GTTCC 707s Processing line... 707s GTTCC 707s GTTCC 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s AG 707s AG 707s Processing line... 707s AG 707s AG 707s Processing line... 707s AG 707s AG 707s Processing line... 707s AG 707s AG 707s Processing line... 707s AG 707s AG 707s Processing line... 707s AG 707s AG 707s Processing line... 707s AG 707s AG 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s CGCCGTTCCCGGTGTGTCG 707s CGCCGTTCCCGGTGTGTCG 707s Processing line... 707s CGCCGTTCCCGGTGTGTCG 707s CGCCGTTCCCGGTGTGTCG 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s CGT 707s CGT 707s Processing line... 707s CGT 707s CGT 707s Processing line... 707s CGT 707s CGT 707s Processing line... 707s CGT 707s CGT 707s Processing line... 707s CGT 707s CGT 707s Processing line... 707s CGT 707s CGT 707s Processing line... 707s CGT 707s CGT 707s Processing line... 707s CGT 707s CGT 707s Processing line... 707s CGT 707s CGT 707s Processing line... 707s CGT 707s CGT 707s Processing line... 707s Processing line... 707s GAGTCCCGCGGCCCG 707s GAGTCCCGCGGCCCG 707s Processing line... 707s Processing line... 707s GAACGT 707s GAACGT 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s ACGT 707s ACGT 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s AGGTTGGAGTCCCGCGGCCCGT 707s AGGTTGGAGTCCCGCGGCCCGT 707s Processing line... 707s GCG 707s GCG 707s Processing line... 707s AGGTTGGAGTCCCGCGGCCCGT 707s AGGTTGGAGTCCCGCGGCCCGT 707s Processing line... 707s GCG 707s GCG 707s Processing line... 707s AGGTTGGAGTCCCGCGGCCCGT 707s AGGTTGGAGTCCCGCGGCCCGT 707s Processing line... 707s GCG 707s GCG 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s GG 707s GG 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s AT 707s AT 707s Processing line... 707s AT 707s AT 707s Processing line... 707s AT 707s AT 707s Processing line... 707s Processing line... 707s GA 707s GA 707s Processing line... 707s GA 707s GA 707s Processing line... 707s GA 707s GA 707s Processing line... 707s GA 707s GA 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s TTTATGTC 707s TTTATGTC 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s TGGTG 707s TGGTG 707s Processing line... 707s TGGTG 707s TGGTG 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s GGTGCGGCGGGGCCAGTTCGATTCGGTTGGT 707s GGTGCGGCGGGGCCAGTTCGATTCGGTTGGT 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s CGGTT 707s CGGTT 707s Processing line... 707s CGGTT 707s CGGTT 707s Processing line... 707s Processing line... 707s TCGGTTGGTTT 707s TCGGTTGGTTT 707s Processing line... 707s TTTGGTGTG 707s TTTGGTGTG 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s GCGTGGGTGCGGCG 707s GCGTGGGTGCGGCG 707s Processing line... 707s Processing line... 707s TGTCGTTGTA 707s TGTCGTTGTA 707s Processing line... 707s TGTCGTTGTA 707s TGTCGTTGTA 707s Processing line... 707s Processing line... 707s GCCAGTTCGATTCGGTTGGT 707s GCCAGTTCGATTCGGTTGGT 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s /usr/bin/bowtie2 --n-ceil 0.104936212729466,1.02361175883887 --norc --np 1 --cp-min 3 -a --large-index --cp-ival 2 -N 1 -L14 --score-min L,2.91769022913821,8.62354453513459 --mm -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s GT 707s GT 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s TTC 707s TTC 707s Processing line... 707s TTC 707s TTC 707s Processing line... 707s TTC 707s TTC 707s Processing line... 707s TTC 707s TTC 707s Processing line... 707s TTC 707s TTC 707s Processing line... 707s TTC 707s TTC 707s Processing line... 707s TTC 707s TTC 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s TCG 707s TCG 707s Processing line... 707s TCCCGCGGCCCGTT 707s TCCCGCGGCCCGTT 707s Processing line... 707s TCG 707s TCG 707s Processing line... 707s TCCCGCGGCCCGTT 707s TCCCGCGGCCCGTT 707s Processing line... 707s TCG 707s TCG 707s Processing line... 707s TCCCGCGGCCCGTT 707s TCCCGCGGCCCGTT 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s Processing line... 707s CGGCGGGGCCAGTTCGATTCGG 707s CGGCGGGGCCAGTTCGATTCGG 707s Processing line... 707s Processing line... 707s Processing line... 707s --- Summary --- 707s Read 1 reference strings 707s Checked 165 alignments, 0 edits 707s --------------- 707s PASSED 707s ALSO checking that bowtie2 and bowtie2-align match up 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 707s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #1 of read '18' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 707s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #2 of read '41' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 707s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #2 of read '47' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 707s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #2 of read '72' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 707s Warning: skipping mate #1 of read '81' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #1 of read '81' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 707s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #1 of read '85' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 707s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (1) 707s Warning: skipping mate #1 of read '96' because it was < 2 characters long 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 707s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 707s 130 reads; of these: 707s 130 (100.00%) were paired; of these: 707s 126 (96.92%) aligned concordantly 0 times 707s 2 (1.54%) aligned concordantly exactly 1 time 707s 2 (1.54%) aligned concordantly >1 times 707s ---- 707s 126 pairs aligned concordantly 0 times; of these: 707s 0 (0.00%) aligned discordantly 1 time 707s ---- 707s 126 pairs aligned 0 times concordantly or discordantly; of these: 707s 252 mates make up the pairs; of these: 707s 222 (88.10%) aligned 0 times 707s 14 (5.56%) aligned exactly 1 time 707s 16 (6.35%) aligned >1 times 707s 14.62% overall alignment rate 707s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 707s Flattened IUPAC characters 707s Mutating sequence Sim.pm.2 707s Introducing 15 SNPs, 1/1 ref/read gaps, and 2 rearrangements 707s Finished SNPs 707s Finished ref gaps 707s Finished read gaps 707s Mutating sequence Sim.pm.1 707s Introducing 0 SNPs, 2/1 ref/read gaps, and 0 rearrangements 707s Finished SNPs 707s Finished ref gaps 707s Finished read gaps 707s Mutated reference genome to subject genome 707s SNPs introduced: 15 707s Reference gaps introduced: 3 707s Read gaps introduced: 2 707s Rearrangements introduced: 2 707s Created read sampler 707s Sampling 53 reads 707s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 707s *** Run 95 of 100 707s /usr/bin/bowtie2 --rfg 2.82287569574287,4.36355647067647 --trim3 4 -N 1 -L19 -i L,0.112586305043584 --local --cp-ival 4 -a --mm --score-min L,2.36516716146805,4.37845700661132 --gbar 13 --cp-min 5 --large-index -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw 707s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 707s parsing sequence Sim.pm.1... 707s parsing sequence Sim.pm.2... 707s Parsed 234 reference bases 708s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '1' because it was < 2 characters long 708s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '10' because it was < 2 characters long 708s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '20' because it was < 2 characters long 708s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '21' because it was < 2 characters long 708s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '22' because it was < 2 characters long 708s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '28' because it was < 2 characters long 708s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '34' because it was < 2 characters long 708s Warning: skipping read '39' because length (1) <= # seed mismatches (1) 708s Warning: skipping read '39' because it was < 2 characters long 708s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '47' because it was < 2 characters long 708s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '49' because it was < 2 characters long 708s 53 reads; of these: 708s 53 (100.00%) were unpaired; of these: 708s 53 (100.00%) aligned 0 times 708s 0 (0.00%) aligned exactly 1 time 708s 0 (0.00%) aligned >1 times 708s 0.00% overall alignment rate 708s Read 50 alignments... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s /usr/bin/bowtie2 --rfg 2.82287569574287,4.36355647067647 --trim3 4 -N 1 -L19 -i L,0.112586305043584 --local --cp-ival 4 -a --mm --score-min L,2.36516716146805,4.37845700661132 --gbar 13 --cp-min 5 --large-index -r -p 3 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s --- Summary --- 708s Read 1 reference strings 708s Checked 0 alignments, 0 edits 708s --------------- 708s PASSED 708s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 708s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '1' because it was < 2 characters long 708s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '10' because it was < 2 characters long 708s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '20' because it was < 2 characters long 708s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '21' because it was < 2 characters long 708s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '22' because it was < 2 characters long 708s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '28' because it was < 2 characters long 708s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '34' because it was < 2 characters long 708s Warning: skipping read '39' because length (1) <= # seed mismatches (1) 708s Warning: skipping read '39' because it was < 2 characters long 708s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '47' because it was < 2 characters long 708s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 708s Warning: skipping read '49' because it was < 2 characters long 708s 53 reads; of these: 708s 53 (100.00%) were unpaired; of these: 708s 53 (100.00%) aligned 0 times 708s 0 (0.00%) aligned exactly 1 time 708s 0 (0.00%) aligned >1 times 708s 0.00% overall alignment rate 708s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 708s Flattened IUPAC characters 708s Mutating sequence Sim.pm.1 708s Introducing 4 SNPs, 0/3 ref/read gaps, and 1 rearrangements 708s Finished SNPs 708s Finished ref gaps 708s Finished read gaps 708s Mutating sequence Sim.pm.2 708s Introducing 20 SNPs, 0/0 ref/read gaps, and 1 rearrangements 708s Finished SNPs 708s Finished ref gaps 708s Finished read gaps 708s Mutated reference genome to subject genome 708s SNPs introduced: 24 708s Reference gaps introduced: 0 708s Read gaps introduced: 3 708s Rearrangements introduced: 2 708s Created read sampler 708s Sampling 83 reads 708s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 708s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 708s parsing sequence Sim.pm.1... 708s parsing sequence Sim.pm.2... 708s Parsed 234 reference bases 708s *** Run 96 of 100 708s /usr/bin/bowtie2 --cp-ival 2 --local --trim5 2 --n-ceil 0.597220309201501,0.132316581321372 --rfg 34.8747467917174,6.79394697420555 --trim3 9 --large-index --cp-min 2 --np 1 --mm -D 31 --score-min L,1.13482315254396,1.0583689021698 -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 708s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '1' because it was < 2 characters long 708s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '3' because it was < 2 characters long 708s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '4' because it was < 2 characters long 708s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '11' because it was < 2 characters long 708s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 708s Warning: skipping read '13' because it was < 2 characters long 708s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '18' because it was < 2 characters long 708s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '26' because it was < 2 characters long 708s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 708s Warning: skipping read '27' because it was < 2 characters long 708s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '30' because it was < 2 characters long 708s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '31' because it was < 2 characters long 708s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '35' because it was < 2 characters long 708s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 708s Warning: skipping read '37' because it was < 2 characters long 708s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '45' because it was < 2 characters long 708s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '49' because it was < 2 characters long 708s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '50' because it was < 2 characters long 708s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '52' because it was < 2 characters long 708s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '53' because it was < 2 characters long 708s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '55' because it was < 2 characters long 708s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 708s Warning: skipping read '57' because it was < 2 characters long 708s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '58' because it was < 2 characters long 708s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '65' because it was < 2 characters long 708s Read 50 alignments... 708s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '69' because it was < 2 characters long 708s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '79' because it was < 2 characters long 708s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 708s Warning: skipping mate #1 of read '82' because it was < 2 characters long 708s 83 reads; of these: 708s 67 (80.72%) were paired; of these: 708s 62 (92.54%) aligned concordantly 0 times 708s 2 (2.99%) aligned concordantly exactly 1 time 708s 3 (4.48%) aligned concordantly >1 times 708s ---- 708s 62 pairs aligned concordantly 0 times; of these: 708s 6 (9.68%) aligned discordantly 1 time 708s ---- 708s 56 pairs aligned 0 times concordantly or discordantly; of these: 708s 112 mates make up the pairs; of these: 708s 83 (74.11%) aligned 0 times 708s 13 (11.61%) aligned exactly 1 time 708s 16 (14.29%) aligned >1 times 708s 16 (19.28%) were unpaired; of these: 708s 12 (75.00%) aligned 0 times 708s 1 (6.25%) aligned exactly 1 time 708s 3 (18.75%) aligned >1 times 708s 36.67% overall alignment rate 708s Read 100 alignments... 708s Read 150 alignments... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s CTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTAGTGACGCCGTTGAACGTGCGGC-GGG 708s CTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCGGCGGGG 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s ACG 708s ACG 708s Processing line... 708s Processing line... 708s TTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCG-T 708s TTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTT 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s GGGGGCGTGGGTGCGGC-GGG 708s GGGGGCGTGGGTGCGGCGGGG 708s Processing line... 708s CCAGGTCGATTCGGT 708s CCAGTTCGATTCGGT 708s Processing line... 708s Processing line... 708s Processing line... 708s GT 708s GT 708s Processing line... 708s Processing line... 708s Processing line... 708s GTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTAGTGA--C 708s GTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGC 708s Processing line... 708s Processing line... 708s TT 708s TT 708s Processing line... 708s Processing line... 708s Processing line... 708s GGTG 708s GGTG 708s Processing line... 708s AACGT 708s AACGT 708s Processing line... 708s GGGCCAGTTCGATTCGGTTGGTTTATCTCATCGCTCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTAGTGACGCCGTTGAACGT--G 708s GGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCG 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s GGAGTCCCGCGGCCCG 708s GGAGTCCCGCGGCCCG 708s Processing line... 708s Processing line... 708s TGGTGTGTACGGG 708s TGGTGTGTNCGGG 708s Processing line... 708s GTTTGGTG 708s GTTTGGTG 708s Processing line... 708s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAG 708s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAG 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s TC 708s TC 708s Processing line... 708s Processing line... 708s GTCGTTGTAGGCCGTTGGGGTTC 708s GTCGTTGTAGGCCGTTGGGGTTC 708s Processing line... 708s TCGCCG 708s TCGCCG 708s Processing line... 708s ATTCGGTTGGTTTATCTCATCGCTCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTAGTGACGCCGTTGAACGT--G 708s ATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCG 708s Processing line... 708s TGGTTTATCTCATCGCTCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCT--AG 708s TGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTG 708s Processing line... 708s GGTTTATGTCAT 708s GGTTTATGTCAT 708s Processing line... 708s Processing line... 708s GTTGGGGTTCGCCGTTCCCGGTGTGTC 708s GTTGGGGTTCGCCGTTCCCGGTGTGTC 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s GCCAGTTCGATTCGGTTGGTTTATGTCATGGCGCGGTTGTTTGGTGTGTAC---G 708s GCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGG 708s Processing line... 708s GGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATCTCATCGCTCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTAGTGACG-C 708s GGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCC 708s Processing line... 708s Processing line... 708s Processing line... 708s GGGCCAGTTCGATTCGGTTGGTTTATCTCATCGCTCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTAGTGACG-C 708s GGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCC 708s Processing line... 708s TTCGATTCGGTTGGTTTATCTCATCGCTCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGT--C 708s TTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCC 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s GGT 708s GGT 708s Processing line... 708s GGGGTTCGCCGTTCCCGGTGTGTC 708s GGGGTTCGCCGTTCCCGGTGTGTC 708s Processing line... 708s GCCAGTTCGATTCGGTTGGTTTA--T 708s GCCAGTTCGATTCGGTTGGTTTATGT 708s Processing line... 708s Processing line... 708s GTG 708s GTG 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTC 708s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTC 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s GTTCGCCGTTCCCGGTGTGTC-GTG 708s GTTCGCCGTTCCCGGTGTGTCGTTG 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s TGTCGTTGTAGACCGTTG 708s TGTCGTTGTAGGCCGTTG 708s Processing line... 708s Processing line... 708s CGCCGTTCCCGGTGTGTCGTTGTAGACCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCCC 708s CGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCCC 708s Processing line... 708s GTGCG 708s GTGCG 708s Processing line... 708s Processing line... 708s Processing line... 708s TGCGG 708s TGCGG 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s CGT 708s CGT 708s Processing line... 708s TCATCGCTCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTAGTGACGCCGTTGAACGT-----G 708s TCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCGGCG 708s Processing line... 708s GCCAGTTCGATTCGGTTGGTTTATGTCAT-G 708s GCCAGTTCGATTCGGTTGGTTTATGTCATCG 708s Processing line... 708s CCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGG 708s CCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGG 708s Processing line... 708s Processing line... 708s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGACCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGT----T 708s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCCCT 708s Processing line... 708s Processing line... 708s GGCGGGGCCAGTTCGATTCGG 708s GGCGGGGCCAGTTCGATTCGG 708s Processing line... 708s Processing line... 708s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATCTCATCGCTCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTAGTGACGCCGTTGAAC--G 708s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTG 708s Processing line... 708s Processing line... 708s GGGGGCGTGGGTGCAGCGGCGCCAGTTCGATTCGGTTGGTTTATGTCATGGCGCGGTTG--T 708s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTT 708s Processing line... 708s GTTGGTTTATCTCATCGCTCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTAGTGACGCCGTTGAACGT-----G 708s GTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCGGCG 708s Processing line... 708s GCGTGGGTGCAGCGGCGCCAGTTCGATTCGGTTGGTTTATGTCAT-G-GC 708s GCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGC 708s Processing line... 708s Processing line... 708s CGTTCCCGGTGTGTC 708s CGTTCCCGGTGTGTC 708s Processing line... 708s Processing line... 708s Processing line... 708s CCGTTCCCGGT 708s CCGTTCCCGGT 708s Processing line... 708s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATCTCATCGCTCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGT---------C 708s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCC 708s Processing line... 708s CGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTAGTGACGCCGTTGAACGTGCGGC-G 708s CGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCGGCGG 708s Processing line... 708s GTTGGGGTTCGCCGTTCCCG 708s GTTGGGGTTCGCCGTTCCCG 708s Processing line... 708s Processing line... 708s TTCCCGGTGTGTCGTTGTAGACCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGG 708s TTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGG 708s Processing line... 708s Processing line... 708s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCG 708s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCG 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s TCATCGCTCGGTTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTAGTGACGCCGTTGAACGT--G 708s TCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCG 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s TTGTTTGGTGTGTACGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTA------GG 708s TTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGG 708s Processing line... 708s --- Summary --- 708s Read 1 reference strings 708s Checked 55 alignments, 0 edits 708s --------------- 708s PASSED 708s Flattened IUPAC characters 708s Mutating sequence Sim.pm.2 708s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 708s Finished SNPs 708s Finished ref gaps 708s Finished read gaps 708s Mutating sequence Sim.pm.1 708s Introducing 17 SNPs, 3/1 ref/read gaps, and 3 rearrangements 708s Finished SNPs 708s Finished ref gaps 708s Finished read gaps 708s Mutated reference genome to subject genome 708s SNPs introduced: 22 708s Reference gaps introduced: 3 708s Read gaps introduced: 1 708s Rearrangements introduced: 3 708s Created read sampler 708s Sampling 80 reads 708s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fasta & /tmp/Sim.pm.RKKEKvBt_2.fasta 708s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 708s parsing sequence Sim.pm.1... 708s parsing sequence Sim.pm.2... 708s Parsed 234 reference bases 708s *** Run 97 of 100 708s /usr/bin/bowtie2 --cp-ival 3 --large-index --cp-min 2 -k 2 --score-min L,1.64716874761942,9.01274496833017 -f -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta 708s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 708s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 708s Warning: skipping read '41' because it was < 2 characters long 708s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 708s 80 reads; of these: 708s 80 (100.00%) were unpaired; of these: 708s 54 (67.50%) aligned 0 times 708s 12 (15.00%) aligned exactly 1 time 708s 14 (17.50%) aligned >1 times 708s 32.50% overall alignment rate 708s Read 50 alignments... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s GGTTGGAGTCCCGCGGCC 708s GGTTGGAGTCCCGCGGCC 708s Processing line... 708s Processing line... 708s Processing line... 708s GGTTGGAGTCCCGCGGCC 708s GGTTGGAGTCCCGCGGCC 708s Processing line... 708s GGGGTTCGCCGTTC 708s GGGGTTCGCCGTTC 708s Processing line... 708s GGGGTTCGCCGTTC 708s GGGGTTCGCCGTTC 708s Processing line... 708s GGTGTGTCGTT 708s GGTGTGTCGTT 708s Processing line... 708s GGTGTGTCGTT 708s GGTGTGTCGTT 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s TGGAGTCCCGC 708s TGGAGTCCCGC 708s Processing line... 708s GGGG 708s GGGG 708s Processing line... 708s GGGG 708s GGGG 708s Processing line... 708s GTGCGGCGGGGCCAGT 708s GTGCGGCGGGGCCAGT 708s Processing line... 708s GTGCGGCGGGGCCAGT 708s GTGCGGCGGGGCCAGT 708s Processing line... 708s Processing line... 708s GAGTCC 708s GAGTCC 708s Processing line... 708s Processing line... 708s Processing line... 708s CGTTCCCGGTGTGTCGTTG 708s CGTTCCCGGTGTGTCGTTG 708s Processing line... 708s CGTTCCCGGTGTGTCGTTG 708s CGTTCCCGGTGTGTCGTTG 708s Processing line... 708s GGG 708s GGG 708s Processing line... 708s GGG 708s GGG 708s Processing line... 708s GGCGGGGCCAGTTCG 708s GGCGGGGCCAGTTCG 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s GTC 708s GTC 708s Processing line... 708s GTC 708s GTC 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s TCAGGT 708s TCAGGT 708s Processing line... 708s Processing line... 708s Processing line... 708s CC 708s CC 708s Processing line... 708s CC 708s CC 708s Processing line... 708s Processing line... 708s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATT 708s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATT 708s Processing line... 708s CCGGTGT 708s CCGGTGT 708s Processing line... 708s CCGGTGT 708s CCGGTGT 708s Processing line... 708s GGTTCCC 708s GGTTCCC 708s Processing line... 708s Processing line... 708s CGTTC 708s CGTTC 708s Processing line... 708s CGTTC 708s CGTTC 708s Processing line... 708s Processing line... 708s TCG 708s TCG 708s Processing line... 708s TCG 708s TCG 708s Processing line... 708s TGCGG 708s TGCGG 708s Processing line... 708s TGCGG 708s TGCGG 708s Processing line... 708s GGGGG 708s GGGGG 708s Processing line... 708s GGGGG 708s GGGGG 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s TTGAACGTGCGGCGGGGC 708s TTGAACGTGCGGCGGGGC 708s Processing line... 708s Processing line... 708s CGTTC 708s CGTTC 708s Processing line... 708s CGTTC 708s CGTTC 708s Processing line... 708s Processing line... 708s CGTGGGTGCGGCGGGGCCAGTTCGAT 708s CGTGGGTGCGGCGGGGCCAGTTCGAT 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s GCGCGGTTGTTTGGT 708s GCGCGGTTGTTTGGT 708s Processing line... 708s TGCGGCGGGGCCAGTTCGATTCGGTTGGTT 708s TGCGGCGGGGCCAGTTCGATTCGGTTGGTT 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s Processing line... 708s /usr/bin/bowtie2 --cp-ival 3 --large-index --cp-min 2 -k 2 --score-min L,1.64716874761942,9.01274496833017 -f -p 3 -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 708s --- Summary --- 708s Read 1 reference strings 708s Checked 40 alignments, 0 edits 708s --------------- 708s PASSED 708s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 708s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 708s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 708s Warning: skipping read '41' because it was < 2 characters long 708s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 708s 80 reads; of these: 708s 80 (100.00%) were unpaired; of these: 708s 54 (67.50%) aligned 0 times 708s 12 (15.00%) aligned exactly 1 time 708s 14 (17.50%) aligned >1 times 708s 32.50% overall alignment rate 708s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 708s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 708s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 708s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 708s /usr/bin/bowtie2 --cp-ival 3 --large-index --cp-min 2 -k 2 --score-min L,1.64716874761942,9.01274496833017 -f -p 3 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 708s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 708s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 708s Warning: skipping read '41' because it was < 2 characters long 708s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 708s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 708s 80 reads; of these: 708s 80 (100.00%) were unpaired; of these: 708s 54 (67.50%) aligned 0 times 708s 12 (15.00%) aligned exactly 1 time 708s 14 (17.50%) aligned >1 times 708s 32.50% overall alignment rate 708s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 708s Flattened IUPAC characters 709s *** Run 98 of 100 709s /usr/bin/bowtie2 --n-ceil 0.781152965220624,0.781026757502591 --cp-ival 3 --mp 8.27591280706813,2.51709497950649 --rfg 15.1712578672715 --large-index --cp-min 6 --np 1 --score-min L,4.98151337189071,1.55020753749071 -D 7 --gbar 22 -R 3 --rdg 33.2454405119002,4.78199804922093 -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw 709s Mutating sequence Sim.pm.1 709s Introducing 6 SNPs, 1/0 ref/read gaps, and 1 rearrangements 709s Finished SNPs 709s Finished ref gaps 709s Finished read gaps 709s Mutating sequence Sim.pm.2 709s Introducing 13 SNPs, 1/2 ref/read gaps, and 3 rearrangements 709s Finished SNPs 709s Finished ref gaps 709s Finished read gaps 709s Mutated reference genome to subject genome 709s SNPs introduced: 19 709s Reference gaps introduced: 2 709s Read gaps introduced: 2 709s Rearrangements introduced: 4 709s Created read sampler 709s Sampling 77 reads 709s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.raw & /tmp/Sim.pm.RKKEKvBt_2.raw 709s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 709s parsing sequence Sim.pm.1... 709s parsing sequence Sim.pm.2... 709s Parsed 234 reference bases 709s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 709s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 709s Warning: skipping read '12' because it was < 2 characters long 709s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 709s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 709s Warning: skipping read '39' because it was < 2 characters long 709s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 709s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 709s Warning: skipping read '65' because it was < 2 characters long 709s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 709s 77 reads; of these: 709s 77 (100.00%) were unpaired; of these: 709s 54 (70.13%) aligned 0 times 709s 10 (12.99%) aligned exactly 1 time 709s 13 (16.88%) aligned >1 times 709s 29.87% overall alignment rate 709s Read 50 alignments... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s TTCGATTCGGTTGGTTTATGTCATCGCGCGGT 709s TTCGATTCGGTTGGTTTATGTCATCGCGCGGT 709s Processing line... 709s Processing line... 709s Processing line... 709s TCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTG 709s TCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTG 709s Processing line... 709s CGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGG 709s CGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGG 709s Processing line... 709s Processing line... 709s Processing line... 709s TG 709s TG 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s GTTCCCGGTGTG 709s GTTCCCGGTGTG 709s Processing line... 709s Processing line... 709s Processing line... 709s GTGTGTC 709s GTGTGTC 709s Processing line... 709s Processing line... 709s Processing line... 709s GGGGCCAG 709s GGGGCCAG 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s GACGCCGTTGAAC 709s GACGCCGTTGAAC 709s Processing line... 709s GACGCCGTTGAAC 709s GACGCCGTTGAAC 709s Processing line... 709s GGG 709s GGG 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s CGGGGGTCTCAGG 709s CGGGGGTCTCAGG 709s /usr/bin/bowtie2 --n-ceil 0.781152965220624,0.781026757502591 --cp-ival 3 --mp 8.27591280706813,2.51709497950649 --rfg 15.1712578672715 --large-index --cp-min 6 --np 1 --score-min L,4.98151337189071,1.55020753749071 -D 7 --gbar 22 -R 3 --rdg 33.2454405119002,4.78199804922093 -r -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.als 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s GC 709s GC 709s Processing line... 709s TGACGCCGTTG 709s TGACGCCGTTG 709s Processing line... 709s Processing line... 709s Processing line... 709s CGTTGAACGTGCGGCG 709s CGTTGAACGTGCGGCG 709s Processing line... 709s TTGGTTTATGTCATCGCGCGGT 709s TTGGTTTATGTCATCGCGCGGT 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s TCCCGGTGTGTCGTTGTAGGCCGTTGGGG 709s TCCCGGTGTGTCGTTGTAGGCCGTTGGGG 709s Processing line... 709s Processing line... 709s Processing line... 709s CGGTGTGTCGTTGTA 709s CGGTGTGTCGTTGTA 709s Processing line... 709s CGCG 709s CGCG 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s GGTTTATGTCATCGCGCGGTTGTTTGGTGTG 709s GGTTTATGTCATCGCGCGGTTGTTTGGTGTG 709s Processing line... 709s Processing line... 709s Processing line... 709s CA 709s CA 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s TTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTA 709s TTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTA 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s Processing line... 709s CG 709s CG 709s Processing line... 709s Processing line... 709s Processing line... 709s GTTC 709s GTTC 709s Processing line... 709s Processing line... 709s --- Summary --- 709s Read 1 reference strings 709s Checked 23 alignments, 0 edits 709s --------------- 709s PASSED 709s ALSO checking that bowtie2 and bowtie2-align match up 709s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 709s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 709s Warning: skipping read '12' because it was < 2 characters long 709s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 709s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 709s Warning: skipping read '39' because it was < 2 characters long 709s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 709s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 709s Warning: skipping read '65' because it was < 2 characters long 709s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 709s 77 reads; of these: 709s 77 (100.00%) were unpaired; of these: 709s 54 (70.13%) aligned 0 times 709s 10 (12.99%) aligned exactly 1 time 709s 13 (16.88%) aligned >1 times 709s 29.87% overall alignment rate 709s diff -uw /tmp/Sim.pm.RKKEKvBt.als /tmp/Sim.pm.RKKEKvBt.debug.als 709s /usr/bin/bowtie2 --n-ceil 0.781152965220624,0.781026757502591 --cp-ival 3 --mp 8.27591280706813,2.51709497950649 --rfg 15.1712578672715 --large-index --cp-min 6 --np 1 --score-min L,4.98151337189071,1.55020753749071 -D 7 --gbar 22 -R 3 --rdg 33.2454405119002,4.78199804922093 -r -p 3 -x /tmp/Sim.pm.RKKEKvBt --reorder /tmp/Sim.pm.RKKEKvBt_1.raw | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.reord.als 709s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 709s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 709s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 709s Warning: skipping read '12' because it was < 2 characters long 709s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 709s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 709s Warning: skipping read '39' because it was < 2 characters long 709s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 709s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 709s Warning: skipping read '65' because it was < 2 characters long 709s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 709s 77 reads; of these: 709s 77 (100.00%) were unpaired; of these: 709s 54 (70.13%) aligned 0 times 709s 10 (12.99%) aligned exactly 1 time 709s 13 (16.88%) aligned >1 times 709s 29.87% overall alignment rate 709s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als /tmp/Sim.pm.RKKEKvBt.px.reord.als 709s Flattened IUPAC characters 709s Mutating sequence Sim.pm.2 709s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 709s Finished SNPs 709s Finished ref gaps 709s Finished read gaps 709s *** Run 99 of 100 709s /usr/bin/bowtie2 --trim5 0 --n-ceil 0.966396140234392,0.0152652372129006 --cp-ival 1 --mp 6.22200709063122,1.16619921574692 --rfg 38.6116196457239,15.535119453671 --np 10 --cp-min 2 --large-index --ma 17.1529893786666 --score-min L,5.54035287021193,7.37648656219307 --rdg 41.2516894617088 --mm -q -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq 709s Mutating sequence Sim.pm.1 709s Introducing 9 SNPs, 2/0 ref/read gaps, and 1 rearrangements 709s Finished SNPs 709s Finished ref gaps 709s Finished read gaps 709s Mutated reference genome to subject genome 709s SNPs introduced: 18 709s Reference gaps introduced: 2 709s Read gaps introduced: 0 709s Rearrangements introduced: 1 709s Created read sampler 709s Sampling 194 reads 709s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 709s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 709s parsing sequence Sim.pm.1... 709s parsing sequence Sim.pm.2... 709s Parsed 234 reference bases 709s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 709s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 709s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 709s Warning: skipping mate #1 of read '1' because it was < 2 characters long 709s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 709s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 710s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '19' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 710s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '30' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of re/usr/bin/bowtie2 --trim5 0 --n-ceil 0.966396140234392,0.0152652372129006 --cp-ival 1 --mp 6.22200709063122,1.16619921574692 --rfg 38.6116196457239,15.535119453671 --np 10 --cp-min 2 --large-index --ma 17.1529893786666 --score-min L,5.54035287021193,7.37648656219307 --rdg 41.2516894617088 --mm -q -p 2 -x /tmp/Sim.pm.RKKEKvBt -1 /tmp/Sim.pm.RKKEKvBt_1.fastq -2 /tmp/Sim.pm.RKKEKvBt_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als 710s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.px.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.px.als.sorted 710s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.RKKEKvBt.debug.als | grep -v '^@PG' > /tmp/Sim.pm.RKKEKvBt.debug.als.sorted 710s diff -uw /tmp/Sim.pm.RKKEKvBt.debug.als.sorted /tmp/Sim.pm.RKKEKvBt.px.als.sorted 710s *** Run 100 of 100 710s /usr/bin/bowtie2 --mm --mp 5.09751649819729,3.76666640451487 --score-min L,9.37227334996836,1.03454161898048 --cp-ival 1 --local --n-ceil 0.712474009515853,0.876111201462081 --cp-min 6 --large-index -a -q -x /tmp/Sim.pm.RKKEKvBt /tmp/Sim.pm.RKKEKvBt_1.fastq 710s *** TEST CASE *** 710s Settings: 710s Output files: "/tmp/Sim.pm.qtk7xXsv.*.bt2l" 710s Line rate: 7 (line is 128 bytes) 710s Lines per side: 1 (side is 128 bytes) 710s Offset rate: 4 (one in 16) 710s FTable chars: 10 710s Strings: unpacked 710s Max bucket size: default 710s Max bucket size, sqrt multiplier: default 710s Max bucket size, len divisor: 8 710s Difference-cover sample period: 1024 710s Endianness: little 710s Actual local endianness: little 710s Sanity checking: disabled 710s Assertions: disabled 710s Random seed: 0 710s Sizeofs: void*:8, int:4, long:8, size_t:8 710s Input files DNA, FASTA: 710s /tmp/Sim.pm.qtk7xXsv.fa 710s Reading reference sizes 710s Time reading reference sizes: 00:00:00 710s Calculating joined length 710s Writing header 710s Reserving space for joined string 710s Joining reference sequences 710s Time to join reference sequences: 00:00:00 710s bmax according to bmaxDivN setting: 5 710s Using parameters --bmax 4 --dcv 1024 710s Doing ahead-of-time memory usage test 710s Passed! Constructing with these parameters: --bmax 4 --dcv 1024 710s Constructing suffix-array element generator 710s Building DifferenceCoverSample 710s Building sPrime 710s Building sPrimeOrder 710s V-Sorting samples 710s V-Sorting samples time: 00:00:00 710s Allocating rank array 710s Ranking v-sort output 710s Ranking v-sort output time: 00:00:00 710s Invoking Larsson-Sadakane on ranks 710s Invoking Larsson-Sadakane on ranks time: 00:00:00 710s Sanity-checking and returning 710s Building samples 710s Reserving space for 28 sample suffixes 710s Generating random suffixes 710s QSorting 28 sample offsets, eliminating duplicates 710s QSorting sample offsets, eliminating duplicates time: 00:00:00 710s Multikey QSorting 19 samples 710s (Using difference cover) 710s Multikey QSorting samples time: 00:00:00 710s Calculating bucket sizes 710s Splitting and merging 710s Splitting and merging time: 00:00:00 710s Avg bucket size: 2.41667 (target: 3) 710s Converting suffix-array elements to index image 710s Allocating ftab, absorbFtab 710s Entering Ebwt loop 710s Getting block 1 of 12 710s Reserving size (4) for bucket 1 710s Calculating Z arrays for bucket 1 710s Entering block accumulator loop for bucket 1: 710s bucket 1: 10% 710s bucket 1: 20% 710s bucket 1: 30% 710s bucket 1: 40% 710s bucket 1: 50% 710s bucket 1: 60% 710s bucket 1: 70% 710s bucket 1: 80% 710s bucket 1: 90% 710s bucket 1: 100% 710s Sorting block of length 3 for bucket 1 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 1 710s Getting block 2 of 12 710s Reserving size (4) for bucket 2 710s Calculating Z arrays for bucket 2 710s Entering block accumulator loop for bucket 2: 710s bucket 2: 10% 710s bucket 2: 20% 710s bucket 2: 30% 710s bucket 2: 40% 710s bucket 2: 50% 710s bucket 2: 60% 710s bucket 2: 70% 710s bucket 2: 80% 710s bucket 2: 90% 710s bucket 2: 100% 710s Sorting block of length 3 for bucket 2 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 2 710s Getting block 3 of 12 710s Reserving size (4) for bucket 3 710s Calculating Z arrays for bucket 3 710s Entering block accumulator loop for bucket 3: 710s bucket 3: 10% 710s bucket 3: 20% 710s bucket 3: 30% 710s bucket 3: 40% 710s bucket 3: 50% 710s bucket 3: 60% 710s bucket 3: 70% 710s bucket 3: 80% 710s bucket 3: 90% 710s bucket 3: 100% 710s Sorting block of length 3 for bucket 3 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 3 710s Getting block 4 of 12 710s Reserving size (4) for bucket 4 710s Calculating Z arrays for bucket 4 710s Entering block accumulator loop for bucket 4: 710s bucket 4: 10% 710s bucket 4: 20% 710s bucket 4: 30% 710s bucket 4: 40% 710s bucket 4: 50% 710s bucket 4: 60% 710s bucket 4: 70% 710s bucket 4: 80% 710s bucket 4: 90% 710s bucket 4: 100% 710s Returning block of 1 for bucket 4 710s Getting block 5 of 12 710s Reserving size (4) for bucket 5 710s Calculating Z arrays for bucket 5 710s Entering block accumulator loop for bucket 5: 710s bucket 5: 10% 710s bucket 5: 20% 710s bucket 5: 30% 710s bucket 5: 40% 710s bucket 5: 50% 710s bucket 5: 60% 710s bucket 5: 70% 710s bucket 5: 80% 710s bucket 5: 90% 710s bucket 5: 100% 710s Sorting block of length 3 for bucket 5 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 5 710s Getting block 6 of 12 710s Reserving size (4) for bucket 6 710s Calculating Z arrays for bucket 6 710s Entering block accumulator loop for bucket 6: 710s bucket 6: 10% 710s bucket 6: 20% 710s bucket 6: 30% 710s bucket 6: 40% 710s bucket 6: 50% 710s bucket 6: 60% 710s bucket 6: 70% 710s bucket 6: 80% 710s bucket 6: 90% 710s bucket 6: 100% 710s Sorting block of length 3 for bucket 6 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 6 710s Getting block 7 of 12 710s Reserving size (4) for bucket 7 710s Calculating Z arrays for bucket 7 710s Entering block accumulator loop for bucket 7: 710s bucket 7: 10% 710s bucket 7: 20% 710s bucket 7: 30% 710s bucket 7: 40% 710s bucket 7: 50% 710s bucket 7: 60% 710s bucket 7: 70% 710s bucket 7: 80% 710s bucket 7: 90% 710s bucket 7: 100% 710s Sorting block of length 1 for bucket 7 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 2 for bucket 7 710s Getting block 8 of 12 710s Reserving size (4) for bucket 8 710s Calculating Z arrays for bucket 8 710s Entering block accumulator loop for bucket 8: 710s bucket 8: 10% 710s bucket 8: 20% 710s bucket 8: 30% 710s bucket 8: 40% 710s bucket 8: 50% 710s bucket 8: 60% 710s bucket 8: 70% 710s bucket 8: 80% 710s bucket 8: 90% 710s bucket 8: 100% 710s Sorting block of length 2 for bucket 8 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 3 for bucket 8 710s Getting block 9 of 12 710s Reserving size (4) for bucket 9 710s Calculating Z arrays for bucket 9 710s Entering block accumulator loop for bucket 9: 710s bucket 9: 10% 710s bucket 9: 20% 710s bucket 9: 30% 710s bucket 9: 40% 710s bucket 9: 50% 710s bucket 9: 60% 710s bucket 9: 70% 710s bucket 9: 80% 710s bucket 9: 90% 710s bucket 9: 100% 710s Sorting block of length 2 for bucket 9 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 3 for bucket 9 710s Getting block 10 of 12 710s Reserving size (4) for bucket 10 710s Calculating Z arrays for bucket 10 710s Entering block accumulator loop for bucket 10: 710s bucket 10: 10% 710s bucket 10: 20% 710s bucket 10: 30% 710s bucket 10: 40% 710s bucket 10: 50% 710s bucket 10: 60% 710s bucket 10: 70% 710s bucket 10: 80% 710s bucket 10: 90% 710s bucket 10: 100% 710s Sorting block of length 3 for bucket 10 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 10 710s Getting block 11 of 12 710s Reserving size (4) for bucket 11 710s Calculating Z arrays for bucket 11 710s Entering block accumulator loop for bucket 11: 710s bucket 11: 10% 710s bucket 11: 20% 710s bucket 11: 30% 710s bucket 11: 40% 710s bucket 11: 50% 710s bucket 11: 60% 710s bucket 11: 70% 710s bucket 11: 80% 710s bucket 11: 90% 710s bucket 11: 100% 710s Sorting block of length 3 for bucket 11 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 11 710s Getting block 12 of 12 710s Reserving size (4) for bucket 12 710s Calculating Z arrays for bucket 12 710s Entering block accumulator loop for bucket 12: 710s bucket 12: 10% 710s bucket 12: 20% 710s bucket 12: 30% 710s bucket 12: 40% 710s bucket 12: 50% 710s bucket 12: 60% 710s bucket 12: 70% 710s bucket 12: 80% 710s bucket 12: 90% 710s bucket 12: 100% 710s Sorting block of length 3 for bucket 12 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 12 710s Exited Ebwt loop 710s fchr[A]: 0 710s fchr[C]: 6 710s fchr[G]: 17 710s fchr[T]: 35 710s fchr[$]: 40 710s Exiting Ebwt::buildToDisk() 710s Returning from initFromVector 710s Wrote 8389083 bytes to primary EBWT file: /tmp/Sim.pm.qtk7xXsv.1.bt2l.tmp 710s Wrote 28 bytes to secondary EBWT file: /tmp/Sim.pm.qtk7xXsv.2.bt2l.tmp 710s Re-opening _in1 and _in2 as input streams 710s Returning from Ebwt constructor 710s Headers: 710s len: 40 710s bwtLen: 41 710s sz: 10 710s bwtSz: 11 710s lineRate: 7 710s offRate: 4 710s offMask: 0xfffffffffffffff0 710s ftabChars: 10 710s eftabLen: 20 710s eftabSz: 160 710s ftabLen: 1048577 710s ftabSz: 8388616 710s offsLen: 3 710s offsSz: 24 710s lineSz: 128 710s sideSz: 128 710s sideBwtSz: 96 710s sideBwtLen: 384 710s numSides: 1 710s numLines: 1 710s ebwtTotLen: 128 710s ebwtTotSz: 128 710s color: 0 710s reverse: 0 710s Total time for call to driver() for forward index: 00:00:00 710s Reading reference sizes 710s Time reading reference sizes: 00:00:00 710s Calculating joined length 710s Writing header 710s Reserving space for joined string 710s Joining reference sequences 710s Time to join reference sequences: 00:00:00 710s Time to reverse reference sequence: 00:00:00 710s bmax according to bmaxDivN setting: 5 710s Using parameters --bmax 4 --dcv 1024 710s Doing ahead-of-time memory usage test 710s Passed! Constructing with these parameters: --bmax 4 --dcv 1024 710s Constructing suffix-array element generator 710s Building DifferenceCoverSample 710s Building sPrime 710s Building sPrimeOrder 710s V-Sorting samples 710s V-Sorting samples time: 00:00:00 710s Allocating rank array 710s Ranking v-sort output 710s Ranking v-sort output time: 00:00:00 710s Invoking Larsson-Sadakane on ranks 710s Invoking Larsson-Sadakane on ranks time: 00:00:00 710s Sanity-checking and returning 710s Building samples 710s Reserving space for 28 sample suffixes 710s Generating random suffixes 710s QSorting 28 sample offsets, eliminating duplicates 710s QSorting sample offsets, eliminating duplicates time: 00:00:00 710s Multikey QSorting 19 samples 710s (Using difference cover) 710s Multikey QSorting samples time: 00:00:00 710s Calculating bucket sizes 710s Splitting and merging 710s Splitting and merging time: 00:00:00 710s Split 2, merged 7; iterating... 710s Splitting and merging 710s Splitting and merging time: 00:00:00 710s Avg bucket size: 2.41667 (target: 3) 710s Converting suffix-array elements to index image 710s Allocating ftab, absorbFtab 710s Entering Ebwt loop 710s Getting block 1 of 12 710s Reserving size (4) for bucket 1 710s Calculating Z arrays for bucket 1 710s Entering block accumulator loop for bucket 1: 710s bucket 1: 10% 710s bucket 1: 20% 710s bucket 1: 30% 710s bucket 1: 40% 710s bucket 1: 50% 710s bucket 1: 60% 710s bucket 1: 70% 710s bucket 1: 80% 710s bucket 1: 90% 710s bucket 1: 100% 710s Sorting block of length 3 for bucket 1 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 1 710s Getting block 2 of 12 710s Reserving size (4) for bucket 2 710s Calculating Z arrays for bucket 2 710s Entering block accumulator loop for bucket 2: 710s bucket 2: 10% 710s bucket 2: 20% 710s bucket 2: 30% 710s bucket 2: 40% 710s bucket 2: 50% 710s bucket 2: 60% 710s bucket 2: 70% 710s bucket 2: 80% 710s bucket 2: 90% 710s bucket 2: 100% 710s Sorting block of length 3 for bucket 2 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 2 710s Getting block 3 of 12 710s Reserving size (4) for bucket 3 710s Calculating Z arrays for bucket 3 710s Entering block accumulator loop for bucket 3: 710s bucket 3: 10% 710s bucket 3: 20% 710s bucket 3: 30% 710s bucket 3: 40% 710s bucket 3: 50% 710s bucket 3: 60% 710s bucket 3: 70% 710s bucket 3: 80% 710s bucket 3: 90% 710s bucket 3: 100% 710s Sorting block of length 3 for bucket 3 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 3 710s Getting block 4 of 12 710s Reserving size (4) for bucket 4 710s Calculating Z arrays for bucket 4 710s Entering block accumulator loop for bucket 4: 710s bucket 4: 10% 710s bucket 4: 20% 710s bucket 4: 30% 710s bucket 4: 40% 710s bucket 4: 50% 710s bucket 4: 60% 710s bucket 4: 70% 710s bucket 4: 80% 710s bucket 4: 90% 710s bucket 4: 100% 710s Sorting block of length 2 for bucket 4 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 3 for bucket 4 710s Getting block 5 of 12 710s Reserving size (4) for bucket 5 710s Calculating Z arrays for bucket 5 710s Entering block accumulator loop for bucket 5: 710s bucket 5: 10% 710s bucket 5: 20% 710s bucket 5: 30% 710s bucket 5: 40% 710s bucket 5: 50% 710s bucket 5: 60% 710s bucket 5: 70% 710s bucket 5: 80% 710s bucket 5: 90% 710s bucket 5: 100% 710s Sorting block of length 2 for bucket 5 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 3 for bucket 5 710s Getting block 6 of 12 710s Reserving size (4) for bucket 6 710s Calculating Z arrays for bucket 6 710s Entering block accumulator loop for bucket 6: 710s bucket 6: 10% 710s bucket 6: 20% 710s bucket 6: 30% 710s bucket 6: 40% 710s bucket 6: 50% 710s bucket 6: 60% 710s bucket 6: 70% 710s bucket 6: 80% 710s bucket 6: 90% 710s bucket 6: 100% 710s Sorting block of length 3 for bucket 6 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 6 710s Getting block 7 of 12 710s Reserving size (4) for bucket 7 710s Calculating Z arrays for bucket 7 710s Entering block accumulator loop for bucket 7: 710s bucket 7: 10% 710s bucket 7: 20% 710s bucket 7: 30% 710s bucket 7: 40% 710s bucket 7: 50% 710s bucket 7: 60% 710s bucket 7: 70% 710s bucket 7: 80% 710s bucket 7: 90% 710s bucket 7: 100% 710s Sorting block of length 3 for bucket 7 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 7 710s Getting block 8 of 12 710s Reserving size (4) for bucket 8 710s Calculating Z arrays for bucket 8 710s Entering block accumulator loop for bucket 8: 710s bucket 8: 10% 710s bucket 8: 20% 710s bucket 8: 30% 710s bucket 8: 40% 710s bucket 8: 50% 710s bucket 8: 60% 710s bucket 8: 70% 710s bucket 8: 80% 710s bucket 8: 90% 710s bucket 8: 100% 710s Sorting block of length 1 for bucket 8 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 2 for bucket 8 710s Getting block 9 of 12 710s Reserving size (4) for bucket 9 710s Calculating Z arrays for bucket 9 710s Entering block accumulator loop for bucket 9: 710s bucket 9: 10% 710s bucket 9: 20% 710s bucket 9: 30% 710s bucket 9: 40% 710s bucket 9: 50% 710s bucket 9: 60% 710s bucket 9: 70% 710s bucket 9: 80% 710s bucket 9: 90% 710s bucket 9: 100% 710s Sorting block of length 2 for bucket 9 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 3 for bucket 9 710s Getting block 10 of 12 710s Reserving size (4) for bucket 10 710s Calculating Z arrays for bucket 10 710s Entering block accumulator loop for bucket 10: 710s bucket 10: 10% 710s bucket 10: 20% 710s bucket 10: 30% 710s bucket 10: 40% 710s bucket 10: 50% 710s bucket 10: 60% 710s bucket 10: 70% 710s bucket 10: 80% 710s bucket 10: 90% 710s bucket 10: 100% 710s Sorting block of length 3 for bucket 10 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 10 710s Getting block 11 of 12 710s Reserving size (4) for bucket 11 710s Calculating Z arrays for bucket 11 710s Entering block accumulator loop for bucket 11: 710s bucket 11: 10% 710s bucket 11: 20% 710s bucket 11: 30% 710s bucket 11: 40% 710s bucket 11: 50% 710s bucket 11: 60% 710s bucket 11: 70% 710s bucket 11: 80% 710s bucket 11: 90% 710s bucket 11: 100% 710s Sorting block of length 3 for bucket 11 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 4 for bucket 11 710s Getting block 12 of 12 710s Reserving size (4) for bucket 12 710s Calculating Z arrays for bucket 12 710s Entering block accumulator loop for bucket 12: 710s bucket 12: 10% 710s bucket 12: 20% 710s bucket 12: 30% 710s bucket 12: 40% 710s bucket 12: 50% 710s bucket 12: 60% 710s bucket 12: 70% 710s bucket 12: 80% 710s bucket 12: 90% 710s bucket 12: 100% 710s Sorting block of length 1 for bucket 12 710s (Using difference cover) 710s Sorting block time: 00:00:00 710s Returning block of 2 for bucket 12 710s Exited Ebwt loop 710s fchr[A]: 0 710s fchr[C]: 6 710s fchr[G]: 17 710s fchr[T]: 35 710s fchr[$]: 40 710s Exiting Ebwt::buildToDisk() 710s Returning from initFromVector 710s Wrote 8389083 bytes to primary EBWT file: /tmp/Sim.pm.qtk7xXsv.rev.1.bt2l.tmp 710s Wrote 28 bytes to secondary EBWT file: /tmp/Sim.pm.qtk7xXsv.rev.2.bt2l.tmp 710s Re-opening _in1 and _in2 as input streams 710s Returning from Ebwt constructor 710s Headers: 710s len: 40 710s bwtLen: 41 710s sz: 10 710s bwtSz: 11 710s lineRate: 7 710s offRate: 4 710s offMask: 0xfffffffffffffff0 710s ftabChars: 10 710s eftabLen: 20 710s eftabSz: 160 710s ftabLen: 1048577 710s ftabSz: 8388616 710s offsLen: 3 710s offsSz: 24 710s lineSz: 128 710s sideSz: 128 710s sideBwtSz: 96 710s sideBwtLen: 384 710s numSides: 1 710s numLines: 1 710s ebwtTotLen: 128 710s ebwtTotSz: 128 710s color: 0 710s reverse: 1 710s Total time for backward call to driver() for mirror index: 00:00:00 710s *** Run 1 of 100 710s /usr/bin/bowtie2 --mm --rdg 37.4747287334651 --score-min L,4.07855984181053,2.82592316307289 --cp-ival 3 --large-index -a --cp-min 2 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 710s /usr/bin/bowtie2 --mm --rdg 37.4747287334651 --score-min L,4.07855984181053,2.82592316307289 --cp-ival 3 --large-index -a --cp-min 2 -q -p 4 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 710s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 710s *** Run 2 of 100 710s /usr/bin/bowtie2 --np 3 --cp-min 2 --large-index --cp-ival 1 --local -N 1 -L24 --trim3 3 --score-min L,7.180194426941,1.96424698734702 --rdg 27.3354814329724,8.46759059035461 --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq 710s ad '36; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 710s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '42' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 710s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '49' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 710s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '56' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 710s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #1 of read '62' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 710s Read 50 alignments... 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 710s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '82' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 710s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '86' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 710s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '91' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 710s Read 100 alignments... 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 710s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '99' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 710s Warning: skipping mate #1 of read '101' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #1 of read '101' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 710s Warning: skipping mate #1 of read '133' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #1 of read '133' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 710s Read 150 alignments... 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 710s Read 200 alignments... 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 710s 194 reads; of these: 710s 194 (100.00%) were paired; of these: 710s 188 (96.91%) aligned concordantly 0 times 710s 1 (0.52%) aligned concordantly exactly 1 time 710s 5 (2.58%) aligned concordantly >1 times 710s ---- 710s 188 pairs aligned concordantly 0 times; of these: 710s 3 (1.60%) aligned discordantly 1 time 710s ---- 710s 185 pairs aligned 0 times concordantly or discordantly; of these: 710s 370 mates make up the pairs; of these: 710s 285 (77.03%) aligned 0 times 710s 37 (10.00%) aligned exactly 1 time 710s 48 (12.97%) aligned >1 times 710s 26.55% overall alignment rate 710s Read 250 alignments... 710s Read 300 alignments... 710s Read 350 alignments... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TC 710s TC 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TGACGCCGTTG 710s TGACGCCGTTG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TGTG 710s TGTG 710s Processing line... 710s Processing line... 710s GGGTTC 710s GGGTTC 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TCG 710s TCG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GGGGCGTGGGTGCGGCGGGGCCA 710s GGGGCGTGGGTGCGGCGGGGCCA 710s Processing line... 710s GCGTGGGTGCGGCGG 710s GCGTGGGTGCGGCGG 710s Processing line... 710s Processing line... 710s Processing line... 710s CGCCGTTGAAC 710s CGCCGTTGAAC 710s Processing line... 710s GTGACGCCGTTGA 710s GTGACGCCGTTGA 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GCGG 710s GCGG 710s Processing line... 710s Processing line... 710s GCCGTTCCCGG 710s GCCGTTCCCGG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GC 710s GC 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TGTGTCGTTGTA 710s TGTGTCGTTGTA 710s Processing line... 710s Processing line... 710s TCGT 710s TCGT 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GGCCAGTTCGATTCGGTTGGTT 710s GGCCAGTTCGATTCGGTTGGTT 710s Processing line... 710s Processing line... 710s GGTGCGGCGGGGCCAGTTCGATTCGGTTG 710s GGTGCGGCGGGGCCAGTTCGATTCGGTTG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s CCGTTCCCGGTGTGTCGTTGTA 710s CCGTTCCCGGTGTGTCGTTGTA 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s CGCCGTTCCCGGTGT 710s CGCCGTTCCCGGTGT 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TTGGGGT 710s TTGGGGT 710s Processing line... 710s Processing line... 710s GCGGTTGTTT 710s GCGGTTGTTT 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s CGGT 710s CGGT 710s Processing line... 710s Processing line... 710s TCTCAGGTTG 710s TCTCAGGTTG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s CGG 710s CGG 710s Processing line... 710s Processing line... 710s GGTGTGTCGTTGTAGGCCGTTG 710s GGTGTGTCGTTGTAGGCCGTTG 710s Processing line... 710s Processing line... 710s TG 710s TG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GGGTTCGCCGTTCCCGGTGTGTCGTT 710s GGGTTCGCCGTTCCCGGTGTGTCGTT 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GGGCCA 710s GGGCCA 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GTT 710s GTT 710s Processing line... 710s Processing line... 710s TTGAACG 710s TTGAACG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TG 710s TG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GTGCGGCGGGGCCAGTTCGATTCGGTTG 710s GTGCGGCGGGGCCAGTTCGATTCGGTTG 710s Processing line... 710s Processing line... 710s GTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGG 710s GTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TGTCGTTGTAGGCCGTTGGG 710s TGTCGTTGTAGGCCGTTGGG 710s Processing line... 710s Processing line... 710s GT 710s GT 710s Processing line... 710s GGGGC 710s GGGGC 710s Processing line... 710s CGATTCGGTTGGTTTATGTC 710s CGATTCGGTTGGTTTATGTC 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s CTGGTGACGCCGTTG 710s CTGGTGACGCCGTTG 710s Processing line... 710s Processing line... 710s GGTTCGCCGTT 710s GGTTCGCCGTT 710s Processing line... 710s Processing line... 710s GGGGGTC 710s GGGGGTC 710s Processing line... 710s Processing line... 710s TCGATTCGGTTGGTTTAT 710s TCGATTCGGTTGGTTTAT 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GGTGTGTCG 710s GGTGTGTCG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TGTAGGCCGTTGGGGTTCCCT 710s TGTAGGCCGTTGGGGTTCCCT 710s Processing line... 710s Processing line... 710s GGGGTCTCAGGTTGGAGTCCCG 710s GGGGTCTCAGGTTGGAGTCCCG 710s Processing line... 710s AC 710s AC 710s Processing line... 710s Processing line... 710s Processing line... 710s CGTT 710s CGTT 710s Processing line... 710s Processing line... 710s CGTTCCCGGTGTG 710s CGTTCCCGGTGTG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GC 710s GC 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GCGGGGCCAGT 710s GCGGGGCCAGT 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s CGT 710s CGT 710s Processing line... 710s Processing line... 710s CCGTTGGGGTTCGCCGT 710s CCGTTGGGGTTCGCCGT 710s Processing line... 710s Processing line... 710s TGGTGACGCCGT 710s TGGTGACGCCGT 710s Processing line... 710s Processing line... 710s GGCCAG 710s GGCCAG 710s Processing line... 710s Processing line... 710s CATCG 710s CATCG 710s Processing line... 710s AG 710s AG 710s Processing line... 710s TCCCG 710s TCCCG 710s Processing line... 710s GC 710s GC 710s Processing line... 710s CCG 710s CCG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GTGGGT 710s GTGGGT 710s Processing line... 710s TCATCGCGCGGTTGTTTGG 710s TCATCGCGCGGTTGTTTGG 710s Processing line... 710s GGTGACGCCGTTGAAC 710s GGTGACGCCGTTGAAC 710s Processing line... 710s Processing line... 710s GGTTCGCCGTTCCCGGTGTGTCGTTGTAG 710s GGTTCGCCGTTCCCGGTGTGTCGTTGTAG 710s Processing line... 710s Processing line... 710s GAACGTGCGGCGG 710s GAACGTGCGGCGG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GGGGCCAG 710s GGGGCCAG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TCCCGG 710s TCCCGG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s CGTTCCCGGTGTGT 710s CGTTCCCGGTGTGT 710s Processing line... 710s Processing line... 710s TTCCCGGTGTG 710s TTCCCGGTGTG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GG 710s GG 710s Processing line... 710s Processing line... 710s TGAACGTGCGGCGGG 710s TGAACGTGCGGCGGG 710s Processing line... 710s Processing line... 710s TGGTGACGCCGTTGAACGTGCGGCGGGGCC 710s TGGTGACGCCGTTGAACGTGCGGCGGGGCC 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GACGCCGTTGAACGTGC 710s GACGCCGTTGAACGTGC 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCC 710s TGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCC 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GTCTCAGGTTGGAGTCC 710s GTCTCAGGTTGGAGTCC 710s Processing line... 710s Processing line... 710s CCAGTTCG 710s CCAGTTCG 710s Processing line... 710s Processing line... 710s GTTGA 710s GTTGA 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s CGTTGTAGGCC 710s CGTTGTAGGCC 710s Processing line... 710s TGGG 710s TGGG 710s Processing line... 710s TTGGA 710s TTGGA 710s Processing line... 710s GTTCGAT 710s GTTCGAT 710s Processing line... 710s GTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCG 710s GTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s AGC 710s AGC 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GGGTTCGCCGTTCC 710s GGGTTCGCCGTTCC 710s Processing line... 710s Processing line... 710s GCCGTTCCCGGTGTGTCGTTGTAGGCCGTTG 710s GCCGTTCCCGGTGTGTCGTTGTAGGCCGTTG 710s Processing line... 710s Processing line... 710s GGG 710s GGG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TC 710s TC 710s Processing line... 710s Processing line... 710s GGGGGTCTCAGGTTGGAGTCCCGCGGCC 710s GGGGGTCTCAGGTTGGAGTCCCGCGGCC 710s Processing line... 710s Processing line... 710s GTGGGTGCGGCGGGGCCAGTTCGA 710s GTGGGTGCGGCGGGGCCAGTTCGA 710s Processing line... 710s Processing line... 710s GTTGG 710s GTTGG 710s Processing line... 710s GTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 710s GTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 710s Processing line... 710s CCCGGTGTGTCGTTGTAGGCCGTTGGGGT 710s CCCGGTGTGTCGTTGTAGGCCGTTGGGGT 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GGTGTGTCGTTGT 710s GGTGTGTCGTTGT 710s Processing line... 710s Processing line... 710s GGTCT 710s GGTCT 710s Processing line... 710s Processing line... 710s TCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCG 710s TCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCG 710s Processing line... 710s Processing line... 710s TT 710s TT 710s Processing line... 710s Processing line... 710s GAACGTGCGGCG 710s GAACGTGCGGCG 710s Processing line... 710s Processing line... 710s GTTGTA 710s GTTGTA 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GTTCGATT 710s GTTCGATT 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GGTGTGTCGTT 710s GGTGTGTCGTT 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s CGATTC 710s CGATTC 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GG 710s GG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GCGGCGGGGCCAG 710s GCGGCGGGGCCAG 710s Processing line... 710s Processing line... 710s CCAGTTCGATTCGGTTGGTTTAT 710s CCAGTTCGATTCGGTTGGTTTAT 710s Processing line... 710s Processing line... 710s AGGCCGTTGGGGTTCGCC 710s AGGCCGTTGGGGTTCGCC 710s Processing line... 710s Processing line... 710s GCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTG 710s GCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTG 710s Processing line... 710s --- Summary --- 710s Read 1 reference strings 710s Checked 103 alignments, 0 edits 710s --------------- 710s PASSED 710s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 710s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 710s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #1 of read '1' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 710s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '19' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 710s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '30' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 710s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '42' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 710s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '49' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 710s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '56' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 710s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #1 of read '62' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 710s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '82' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 710s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '86' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 710s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '99' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 710s Warning: skipping mate #1 of read '101' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #1 of read '101' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 710s Warning: skipping mate #1 of read '133' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #1 of read '133' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 710s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (0) 710s Warning: skipping mate #2 of read '91' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 710s 194 reads; of these: 710s 194 (100.00%) were paired; of these: 710s 188 (96.91%) aligned concordantly 0 times 710s 1 (0.52%) aligned concordantly exactly 1 time 710s 5 (2.58%) aligned concordantly >1 times 710s ---- 710s 188 pairs aligned concordantly 0 times; of these: 710s 3 (1.60%) aligned discordantly 1 time 710s ---- 710s 185 pairs aligned 0 times concordantly or discordantly; of these: 710s 370 mates make up the pairs; of these: 710s 285 (77.03%) aligned 0 times 710s 37 (10.00%) aligned exactly 1 time 710s 48 (12.97%) aligned >1 times 710s 26.55% overall alignment rate 710s Flattened IUPAC characters 710s Mutating sequence Sim.pm.1 710s Introducing 6 SNPs, 1/1 ref/read gaps, and 0 rearrangements 710s Finished SNPs 710s Finished ref gaps 710s Finished read gaps 710s Mutating sequence Sim.pm.2 710s Introducing 4 SNPs, 1/1 ref/read gaps, and 2 rearrangements 710s Finished SNPs 710s Finished ref gaps 710s Finished read gaps 710s Mutated reference genome to subject genome 710s SNPs introduced: 10 710s Reference gaps introduced: 2 710s Read gaps introduced: 2 710s Rearrangements introduced: 2 710s Created read sampler 710s Sampling 64 reads 710s Dumping reads to temporary files /tmp/Sim.pm.RKKEKvBt_1.fastq & /tmp/Sim.pm.RKKEKvBt_2.fastq 710s Parsing FASTA file /tmp/Sim.pm.RKKEKvBt.fa... 710s parsing sequence Sim.pm.1... 710s parsing sequence Sim.pm.2... 710s Parsed 234 reference bases 710s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 710s Warning: skipping read '25' because it was < 2 characters long 710s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 710s Warning: skipping read '30' because it was < 2 characters long 710s 64 reads; of these: 710s 64 (100.00%) were unpaired; of these: 710s 35 (54.69%) aligned 0 times 710s 19 (29.69%) aligned exactly 1 time 710s 10 (15.62%) aligned >1 times 710s 45.31% overall alignment rate 710s Read 50 alignments... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTGGTGACGCCGTTGAACGTGCGCCGGGG 710s GGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTG---CGGCG 710s Processing line... 710s GGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTGGTGACGCCGTTGAACGTGCGCCGGGG 710s GGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTG---CGGCG 710s Processing line... 710s GTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGGTTGGAGTCCCGCTGCCCGTT------C 710s GTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGC 710s Processing line... 710s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTGGTGACGCCGTT-------------G 710s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTGGTGACGCCGTTGAACGTGCGGCGGG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TCGCCGTTCCCGGTGTGTCGTTGTAGGCC 710s TCGCCGTTCCCGGTGTGTCGTTGTAGGCC 710s Processing line... 710s TCGCCGTTCCCGGTGTGTCGTTGTAGGCC 710s TCGCCGTTCCCGGTGTGTCGTTGTAGGCC 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s CGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCCCT 710s CGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGT----T 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 710s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 710s Processing line... 710s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 710s GGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT 710s Processing line... 710s GGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGGTCGCCGTTCC 710s GGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCC 710s Processing line... 710s GGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGG 710s GGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTT-GG 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s TTGTAGGCCGTTGGGGGTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGT----T 710s TTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCCCT 710s Processing line... 710s GTTGGGGGTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGC----C 710s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTC 710s Processing line... 710s TGGTTTATGTCATCGCGCGGTTG 710s TGGTTTATGTCATCGCGCGGTTG 710s Processing line... 710s Processing line... 710s Processing line... 710s TTTATGTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTAGGTAGCGGTCTGGTG 710s TTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAGTCCCGCGGCCCGTTNGGTAGCGGNCTG--G 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s GAGTCCCGCGGCC 710s GAGTCCCGCGGCC 710s Processing line... 710s Processing line... 710s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTA-GTCATCGCGCGGTTG 710s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTG 710s Processing line... 710s Processing line... 710s GTTGGGGTTCGCCGTTCCCGGTGTGTC 710s GTTGGGGTTCGCCGTTCCCGGTGTGTC 710s Processing line... 710s GTTGGGGTTCGCCGTTCCCGGTGTGTC 710s GTTGGGGTTCGCCGTTCCCGGTGTGTC 710s Processing line... 710s Processing line... 710s TGGTTTATGTCATCGCGCGGTTG 710s TGGTTTATGTCATCGCGCGGTTG 710s Processing line... 710s Processing line... 710s TGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTCCC 710s TGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTT-CC 710s Processing line... 710s GCCGTTGGGGGTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGG 710s GCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGG 710s Processing line... 710s GTTGGGGGTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGG 710s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCG-TTG 710s Processing line... 710s Processing line... 710s Processing line... 710s GATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGGTT---G 710s GATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTTGGAG 710s Processing line... 710s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTTC-GG 710s GGGGGCGTGGGTGCGGCGGGGCCAGTTCGATTCGGTTGGTTTATGTCATCGCGCGGTTGTTTGGTGTGTNCGGG 710s Processing line... 710s GTCATCGCGCGG 710s GTCATCGCGCGG 710s Processing line... 710s CAGTTCGATTCGGTTGGTTTA-GT 710s CAGTTCGATTCGGTTGGTTTATGT 710s Processing line... 710s TGTCATCGCGCG 710s TGTCATCGCGCG 710s Processing line... 710s Processing line... 710s GTTGGAGTCCCG 710s GTTGGAGTCCCG 710s Processing line... 710s Processing line... 710s GGTGTGTCGTTGTA 710s GGTGTGTCGTTGTA 710s Processing line... 710s GGTGTGTCGTTGTA 710s GGTGTGTCGTTGTA 710s Processing line... 710s Processing line... 710s TGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGT 710s TGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGT 710s Processing line... 710s GGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCC 710s GGTGTGTCGTTGTAGGCCGTTGGGGTTCGCCGTTCCC 710s Processing line... 710s GGTGTGTCGTTGTAGGCCGTTGGGGTTCGCC 710s GGTGTGTCGTTGTAGGCCGTTGGGGTTC-CC 710s Processing line... 710s Processing line... 710s CATCGCGCGGTTGTTTGGTGTGTTCGGGGGTCTCAGG-T 710s CATCGCGCGGTTGTTTGGTGTGTNCGGGGGTCTCAGGTT 710s Processing line... 710s GTTGGGGTACGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 710s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTTC 710s Processing line... 710s GTTGGGGTACGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTT 710s GTTGGGGTTCGCCGTTCCCGGTGTGTCGTTGTAGGCCGTTGGGGTT 710s Processing line... 710s GGTTCGCCGTTCCCGGTG 710s GGTTCGCCGTTCCCGGTG 710s Processing line... 710s GGTTCGCCGTTCCCGGTG 710s GGTTCGCCGTTCCCGGTG 710s --- Summary --- 710s Read 1 reference strings 710s Checked 39 alignments, 0 edits 710s --------------- 710s PASSED 710s Created DNA generator 710s N frac: 0.009 710s IUPAC frac: 0.010 710s AT/ACGT frac: 0.328 710s A/AT frac: 0.269 710s C/CG frac: 0.283 710s Generating 2 references 710s Generated reference 'Sim.pm.1' of untrimmed length 297, trimmed length 19 710s Generated reference 'Sim.pm.2' of untrimmed length 125, trimmed length 21 710s Wrote references to /tmp/Sim.pm.qtk7xXsv.fa 710s A: 6 710s C: 11 710s G: 18 710s T: 5 710s Executing: /usr/bin/bowtie2-build --large-index --threads 2 /tmp/Sim.pm.qtk7xXsv.fa /tmp/Sim.pm.qtk7xXsv 710s Building a LARGE index 710s Renaming /tmp/Sim.pm.qtk7xXsv.3.bt2l.tmp to /tmp/Sim.pm.qtk7xXsv.3.bt2l 710s Renaming /tmp/Sim.pm.qtk7xXsv.4.bt2l.tmp to /tmp/Sim.pm.qtk7xXsv.4.bt2l 710s Renaming /tmp/Sim.pm.qtk7xXsv.1.bt2l.tmp to /tmp/Sim.pm.qtk7xXsv.1.bt2l 710s Renaming /tmp/Sim.pm.qtk7xXsv.2.bt2l.tmp to /tmp/Sim.pm.qtk7xXsv.2.bt2l 710s Renaming /tmp/Sim.pm.qtk7xXsv.rev.1.bt2l.tmp to /tmp/Sim.pm.qtk7xXsv.rev.1.bt2l 710s Renaming /tmp/Sim.pm.qtk7xXsv.rev.2.bt2l.tmp to /tmp/Sim.pm.qtk7xXsv.rev.2.bt2l 710s Built nucleotide index '/tmp/Sim.pm.qtk7xXsv' 710s Flattened IUPAC characters 710s Mutating sequence Sim.pm.2 710s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 710s Finished SNPs 710s Finished ref gaps 710s Finished read gaps 710s Mutating sequence Sim.pm.1 710s Introducing 8 SNPs, 2/0 ref/read gaps, and 2 rearrangements 710s Finished SNPs 710s Finished ref gaps 710s Finished read gaps 710s Mutated reference genome to subject genome 710s SNPs introduced: 10 710s Reference gaps introduced: 3 710s Read gaps introduced: 0 710s Rearrangements introduced: 2 710s Created read sampler 710s Sampling 29 reads 710s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 710s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 710s parsing sequence Sim.pm.1... 710s parsing sequence Sim.pm.2... 710s Parsed 40 reference bases 710s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 710s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 710s Warning: skipping read '20' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 710s 29 reads; of these: 710s 29 (100.00%) were unpaired; of these: 710s 28 (96.55%) aligned 0 times 710s 0 (0.00%) aligned exactly 1 time 710s 1 (3.45%) aligned >1 times 710s 3.45% overall alignment rate 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s CG 710s CG 710s Processing line... 710s CG 710s CG 710s Processing line... 710s CG 710s CG 710s Processing line... 710s CG 710s CG 710s Processing line... 710s CG 710s CG 710s Processing line... 710s CG 710s CG 710s Processing line... 710s CG 710s CG 710s Processing line... 710s CG 710s CG 710s Processing line... 710s CG 710s CG 710s Processing line... 710s CG 710s CG 710s Processing line... 710s CG 710s CG 710s Processing line... 710s CG 710s CG 710s Processing line... 710s Processing line... 710s --- Summary --- 710s Read 1 reference strings 710s Checked 12 alignments, 0 edits 710s --------------- 710s PASSED 710s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 710s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 710s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 710s Warning: skipping read '20' because it was < 2 characters long 710s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 710s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 710s 29 reads; of these: 710s 29 (100.00%) were unpaired; of these: 710s 28 (96.55%) aligned 0 times 710s 0 (0.00%) aligned exactly 1 time 710s 1 (3.45%) aligned >1 times 710s 3.45% overall alignment rate 710s Flattened IUPAC characters 710s Mutating sequence Sim.pm.1 710s Introducing 9 SNPs, 1/0 ref/read gaps, and 1 rearrangements 710s Finished SNPs 710s Finished ref gaps 710s Finished read gaps 710s Mutating sequence Sim.pm.2 710s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 710s Finished SNPs 710s Finished ref gaps 710s Finished read gaps 710s Mutated reference genome to subject genome 710s SNPs introduced: 11 710s Reference gaps introduced: 1 710s Read gaps introduced: 1 710s Rearrangements introduced: 2 710s Created read sampler 710s Sampling 69 reads 710s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 710s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 710s parsing sequence Sim.pm.1... 710s parsing sequence Sim.pm.2... 710s Parsed 40 reference bases 710s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (1) 710s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 710s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (1) 710s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 710s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (1) 710s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 710s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (1) 710s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 710s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (1) 710s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 710s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (1) 710s Read 50 alignments... 710s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 710s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (1) 710s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 710s 69 reads; of these: 710s 64 (92.75%) were paired; of these: 710s 64 (100.00%) aligned concordantly 0 times 710s 0 (0.00%) aligned concordantly exactly 1 time 710s 0 (0.00%) aligned concordantly >1 times 710s ---- 710s 64 pairs aligned concordantly 0 times; of these: 710s 0 (0.00%) aligned discordantly 1 time 710s ---- 710s 64 pairs aligned 0 times concordantly or discordantly; of these: 710s 128 mates make up the pairs; of these: 710s 128 (100.00%) aligned 0 times 710s 0 (0.00%) aligned exactly 1 time 710s 0 (0.00%) aligned >1 times 710s 5 (7.25%) were unpaired; of these: 710s 5 (100.00%) aligned 0 times 710s 0 (0.00%) aligned exactly 1 time 710s 0 (0.00%) aligned >1 times 710s 0.00% overall alignment rate 710s Read 100 alignments... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s Processing line... 710s --- Summary --- 710s Read 1 reference strings 710s Checked 0 alignments, 0 edits 710s --------------- 710s PASSED 710s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 710s /usr/bin/bowtie2 --np 3 --cp-min 2 --large-index --cp-ival 1 --local -N 1 -L24 --trim3 3 --score-min L,7.180194426941,1.96424698734702 --rdg 27.3354814329724,8.46759059035461 --qseq -p 3 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 710s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (1) 710s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 710s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (1) 710s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 710s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (1) 710s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 710s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (1) 710s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 710s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (1) 710s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 710s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (1) 710s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 710s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (1) 710s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 710s 69 reads; of these: 710s 64 (92.75%) were paired; of these: 710s 64 (100.00%) aligned concordantly 0 times 710s 0 (0.00%) aligned concordantly exactly 1 time 710s 0 (0.00%) aligned concordantly >1 times 710s ---- 710s 64 pairs aligned concordantly 0 times; of these: 710s 0 (0.00%) aligned discordantly 1 time 710s ---- 710s 64 pairs aligned 0 times concordantly or discordantly; of these: 710s 128 mates make up the pairs; of these: 710s 128 (100.00%) aligned 0 times 710s 0 (0.00%) aligned exactly 1 time 710s 0 (0.00%) aligned >1 times 710s 5 (7.25%) were unpaired; of these: 710s 5 (100.00%) aligned 0 times 710s 0 (0.00%) aligned exactly 1 time 710s 0 (0.00%) aligned >1 times 710s 0.00% overall alignment rate 710s Flattened IUPAC characters 710s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 710s Mutating sequence Sim.pm.1 710s Introducing 5 SNPs, 0/0 ref/read gaps, and 2 rearrangements 710s *** Run 3 of 100 710s /usr/bin/bowtie2 --cp-ival 1 -N 0 -L17 --trim3 0 --nofw --large-index --np 1 --cp-min 2 -D 32 -R 1 --score-min L,1.7028119888804,5.80955935586828 --ma 3.04754124211194 --mm --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq 710s Finished SNPs 710s Finished ref gaps 710s Finished read gaps 710s Mutating sequence Sim.pm.2 710s Introducing 4 SNPs, 0/2 ref/read gaps, and 0 rearrangements 710s Finished SNPs 710s Finished ref gaps 710s Finished read gaps 710s Mutated reference genome to subject genome 710s SNPs introduced: 9 710s Reference gaps introduced: 0 710s Read gaps introduced: 2 710s Rearrangements introduced: 2 710s Created read sampler 710s Sampling 21 reads 710s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 710s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 710s parsing sequence Sim.pm.1... 710s parsing sequence Sim.pm.2... 710s Parsed 40 reference bases 711s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 711s 21 reads; of these: 711s 21 (100.00%) were unpaired; of these: 711s 18 (85.71%) aligned 0 times 711s 1 (4.76%) aligned exactly 1 time 711s 2 (9.52%) aligned >1 times 711s 14.29% overall alignment rate 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s CC 711s CC 711s Processing line... 711s GCGAC 711s GCGAC 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s AC 711s AC 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s --- Summary --- 711s Read 1 reference strings 711s Checked 3 alignments, 0 edits 711s --------------- 711s PASSED 711s ALSO checking that bowtie2 and bowtie2-align match up 711s /usr/bin/bowtie2 --cp-ival 1 -N 0 -L17 --trim3 0 --nofw --large-index --np 1 --cp-min 2 -D 32 -R 1 --score-min L,1.7028119888804,5.80955935586828 --ma 3.04754124211194 --mm --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 711s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 711s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 711s /usr/bin/bowtie2 --cp-ival 1 -N 0 -L17 --trim3 0 --nofw --large-index --np 1 --cp-min 2 -D 32 -R 1 --score-min L,1.7028119888804,5.80955935586828 --ma 3.04754124211194 --mm --qseq -p 3 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 711s 21 reads; of these: 711s 21 (100.00%) were unpaired; of these: 711s 18 (85.71%) aligned 0 times 711s 1 (4.76%) aligned exactly 1 time 711s 2 (9.52%) aligned >1 times 711s 14.29% overall alignment rate 711s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 711s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 711s 21 reads; of these: 711s 21 (100.00%) were unpaired; of these: 711s 18 (85.71%) aligned 0 times 711s 1 (4.76%) aligned exactly 1 time 711s 2 (9.52%) aligned >1 times 711s 14.29% overall alignment rate 711s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 711s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 711s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 711s /usr/bin/bowtie2 --cp-ival 1 -N 0 -L17 --trim3 0 --nofw --large-index --np 1 --cp-min 2 -D 32 -R 1 --score-min L,1.7028119888804,5.80955935586828 --ma 3.04754124211194 --mm --qseq -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 711s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 711s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 711s 21 reads; of these: 711s 21 (100.00%) were unpaired; of these: 711s 18 (85.71%) aligned 0 times 711s 1 (4.76%) aligned exactly 1 time 711s 2 (9.52%) aligned >1 times 711s 14.29% overall alignment rate 711s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 711s Flattened IUPAC characters 711s Mutating sequence Sim.pm.1 711s Introducing 12 SNPs, 0/0 ref/read gaps, and 1 rearrangements 711s Finished SNPs 711s Finished ref gaps 711s Finished read gaps 711s Mutating sequence Sim.pm.2 711s Introducing 0 SNPs, 1/3 ref/read gaps, and 0 rearrangements 711s Finished SNPs 711s Finished ref gaps 711s Finished read gaps 711s Mutated reference genome to subject genome 711s SNPs introduced: 12 711s Reference gaps introduced: 1 711s Read gaps introduced: 3 711s Rearrangements introduced: 1 711s Created read sampler 711s Sampling 25 reads 711s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 711s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 711s parsing sequence Sim.pm.1... 711s parsing sequence Sim.pm.2... 711s Parsed 40 reference bases 711s *** Run 4 of 100 711s /usr/bin/bowtie2 --large-index --cp-min 2 --rdg 17.3986347051728 --mm --score-min L,9.23862698314865,3.73644371218873 -k 6 -R 1 --local --cp-ival 1 --trim5 5 --nofw --trim3 1 -i C --mp 9.86560462628323,5.75973283712626 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 711s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 711s Warning: skipping read '1' because it was < 2 characters long 711s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 711s Warning: skipping read '7' because it was < 2 characters long 711s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 711s Warning: skipping read '12' because it was < 2 characters long 711s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 711s Warning: skipping read '13' because it was < 2 characters long 711s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 711s Warning: skipping read '22' because it was < 2 characters long 711s 25 reads; of these: 711s 25 (100.00%) were unpaired; of these: 711s 25 (100.00%) aligned 0 times 711s 0 (0.00%) aligned exactly 1 time 711s 0 (0.00%) aligned >1 times 711s 0.00% overall alignment rate 711s Processing line... 711s /usr/bin/bowtie2 --large-index --cp-min 2 --rdg 17.3986347051728 --mm --score-min L,9.23862698314865,3.73644371218873 -k 6 -R 1 --local --cp-ival 1 --trim5 5 --nofw --trim3 1 -i C --mp 9.86560462628323,5.75973283712626 -r -p 3 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s --- Summary --- 711s Read 1 reference strings 711s Checked 0 alignments, 0 edits 711s --------------- 711s PASSED 711s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 711s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 711s Warning: skipping read '1' because it was < 2 characters long 711s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 711s Warning: skipping read '7' because it was < 2 characters long 711s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 711s Warning: skipping read '12' because it was < 2 characters long 711s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 711s Warning: skipping read '13' because it was < 2 characters long 711s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 711s Warning: skipping read '22' because it was < 2 characters long 711s 25 reads; of these: 711s 25 (100.00%sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 711s ) were unpaired; of these: 711s 25 (100.00%) aligned 0 times 711s 0 (0.00%) aligned exactly 1 time 711s 0 (0.00%) aligned >1 times 711s 0.00% overall alignment rate 711s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 711s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 711s Flattened IUPAC characters 711s *** Run 5 of 100 711s /usr/bin/bowtie2 --score-min L,2.0906920040533,8.74009412802197 -D 37 -N 1 -L26 --mp 7.77267444770659,5.25046405442499 --rdg 8.13838289713606,5.67659004941124 --rfg 28.2632812533429,19.5496101568997 --mm --large-index --cp-min 3 --trim5 5 --cp-ival 1 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 711s Mutating sequence Sim.pm.2 711s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 711s Finished SNPs 711s Finished ref gaps 711s Finished read gaps 711s Mutating sequence Sim.pm.1 711s Introducing 8 SNPs, 0/3 ref/read gaps, and 0 rearrangements 711s Finished SNPs 711s Finished ref gaps 711s Finished read gaps 711s Mutated reference genome to subject genome 711s SNPs introduced: 8 711s Reference gaps introduced: 1 711s Read gaps introduced: 3 711s Rearrangements introduced: 0 711s Created read sampler 711s Sampling 91 reads 711s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 711s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 711s parsing sequence Sim.pm.1... 711s parsing sequence Sim.pm.2... 711s Parsed 40 reference bases 711s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 711s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '5' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 711s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '7' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 711s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '10' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 711s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '12' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 711s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '13' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 711s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '21' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 711s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '30' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 711s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '31' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 711s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '40' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 711s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '43' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 711s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '44' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 711s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '51' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 711s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '52' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 711s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '59' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 711s Warning: skipping read '63' because length (1) <= # seed mismatches (1) 711s Warning: skipping read '63' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 711s Warning: skipping read '65' because length (1) <= # seed mismatches (1) 711s Warning: skipping read '65' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 711s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '70' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 711s Warning: skipping read '78' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '78' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 711s Warning: skipping read '79' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '79' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 711s Warning: skipping read '85' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '85' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 711s Warning: skipping read '87' because length (0) <= # seed mismatches (1) 711s Warning: skipping read '87' because it was < 2 characters long 711s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 711s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 711s 91 reads; of these: 711s 91 (100.00%) were unpaired; of these: 711s 84 (92.31%) aligned 0 times 711s 1 (1.10%) aligned exactly 1 time 711s 6 (6.59%) aligned >1 times 711s 7.69% overall alignment rate 711s Read 50 alignments... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s GC 711s GC 711s Processing line... 711s Processing line... 711s GC 711s GC 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s GC 711s GC 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s GGG 711s GGG 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s *** Run 6 of 100 711s /usr/bin/bowtie2 --score-min L,8.10843878761739,7.81192320539312 --mm --large-index --np 1 --cp-min 2 -i S,2.08753002129498 --nofw --rfg 12.7984780123786,10.5907939179882 --norc --n-ceil 0.401603455718744,0.402695005866268 -a --cp-ival 1 --local -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s CCG 711s CCG 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s TT 711s TT 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s AC 711s AC 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s --- Summary --- 711s Read 1 reference strings 711s Checked 7 alignments, 0 edits 711s --------------- 711s PASSED 711s Flattened IUPAC characters 711s Mutating sequence Sim.pm.2 711s Introducing 4 SNPs, 3/0 ref/read gaps, and 0 rearrangements 711s Finished SNPs 711s Finished ref gaps 711s Finished read gaps 711s Mutating sequence Sim.pm.1 711s Introducing 6 SNPs, 1/0 ref/read gaps, and 4 rearrangements 711s Finished SNPs 711s Finished ref gaps 711s Finished read gaps 711s Mutated reference genome to subject genome 711s SNPs introduced: 10 711s Reference gaps introduced: 4 711s Read gaps introduced: 0 711s Rearrangements introduced: 4 711s Created read sampler 711s Sampling 100 reads 711s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 711s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 711s parsing sequence Sim.pm.1... 711s parsing sequence Sim.pm.2... 711s Parsed 40 reference bases 711s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 711s Warning: skipping mate #2 of read '3' because it was < 2 characters long 711s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 711s Warning: skipping mate #1 of read '5' because it was < 2 characters long 711s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 711s Warning: skipping mate #1 of read '28' because it was < 2 characters long 711s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 711s Warning: skipping mate #2 of read '40' because it was < 2 characters long 711s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (0) 711s Warning: skipping mate #1 of read '56' because it was < 2 characters long 711s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (0) 711s Warning: skipping mate #2 of read '73' because it was < 2 characters long 711s Read 50 alignments... 711s Read 100 alignments... 711s Warning: skipping mate #2 of read '84' because length (1) <= # seed mismatches (0) 711s Warning: skipping mate #2 of read '84' because it was < 2 characters long 711s 100 reads; of these: 711s 100 (100.00%) were paired; of these: 711s 100 (100.00%) aligned concordantly 0 times 711s 0 (0.00%) aligned concordantly exactly 1 time 711s 0 (0.00%) aligned concordantly >1 times 711s ---- 711s 100 pairs aligned concordantly 0 times; of these: 711s 0 (0.00%) aligned discordantly 1 time 711s ---- 711s 100 pairs aligned 0 times concordantly or discordantly; of these: 711s 200 mates make up the pairs; of these: 711s 200 (100.00%) aligned 0 times 711s 0 (0.00%) aligned exactly 1 time 711s 0 (0.00%) aligned >1 times 711s 0.00% overall alignment rate 711s Read 150 alignments... 711s Read 200 alignments... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s Processing line... 711s --- Summary --- 711s Read 1 reference strings 711s Checked 0 alignments, 0 edits 711s --------------- 711s PASSED 711s Flattened IUPAC characters 711s Mutating sequence Sim.pm.1 711s Introducing 2 SNPs, 1/1 ref/read gaps, and 2 rearrangements 711s Finished SNPs 711s Finished ref gaps 711s Finished read gaps 711s Mutating sequence Sim.pm.2 711s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 711s Finished SNPs 711s Finished ref gaps 711s Finished read gaps 711s Mutated reference genome to subject genome 711s SNPs introduced: 2 711s Reference gaps introduced: 1 711s Read gaps introduced: 1 711s Rearrangements introduced: 3 711s Created read sampler 711s Sampling 97 reads 711s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 711s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 711s parsing sequence Sim.pm.1... 711s parsing sequence Sim.pm.2... 711s Parsed 40 reference bases 711s *** Run 7 of 100 711s /usr/bin/bowtie2 --trim3 3 --score-min L,8.35830530918015,5.22248143419201 --gbar 3 --mm --rfg 47.9976939665172 --cp-min 5 --large-index --n-ceil 1.32340925372661,0.177369486576135 --trim5 9 --cp-ival 1 -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 712s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 712s Warning: skipping read '4' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 712s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '12' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 712s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 712s Warning: skipping mate #2 of read '18' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 712s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '27' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 712s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '28' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 712s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '33' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 712s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '50' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 712s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '53' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 712s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '55' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 712s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '58' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 712s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '62' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 712s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '63' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 712s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '64' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 712s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #2 of read '69' because length (1) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '69' because it was < 2 characters long 712s Warning: skipping mate #2 of read '69' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 712s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '70' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 712s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 712s Warning: skipping read '74' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 712s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '75' because it was < 2 characters long 712s Warning: skipping mate #2 of read '75' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 712s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '87' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 712s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '96' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 712s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '97' because it was < 2 characters long 712s 97 reads; of these: 712s 80 (82.47%) were paired; of these: 712s 79 (98.75%) aligned concordantly 0 times 712s 0 (0.00%) aligned concordantly exactly 1 time 712s 1 (1.25%) aligned concordantly >1 times 712s ---- 712s 79 pairs aligned concordantly 0 times; of these: 712s 0 (0.00%) aligned discordantly 1 time 712s ---- 712s 79 pairs aligned 0 times concordantly or discordantly; of these: 712s 158 mates make up the pairs; of these: 712s 150 (94.94%) aligned 0 times 712s 4 (2.53%) aligned exactly 1 time 712s 4 (2.53%) aligned >1 times 712s 17 (17.53%) were unpaired; of these: 712s 15 (88.24%) aligned 0 times 712s 1 (5.88%) aligned exactly 1 time 712s 1 (5.88%) aligned >1 times 712s 6.78% overall alignment rate 712s Read 50 alignments... 712s Read 100 alignments... 712s Read 150 alignments... 712s Processing line... 712s /usr/bin/bowtie2 --trim3 3 --score-min L,8.35830530918015,5.22248143419201 --gbar 3 --mm --rfg 47.9976939665172 --cp-min 5 --large-index --n-ceil 1.32340925372661,0.177369486576135 --trim5 9 --cp-ival 1 -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s GAGG 712s GAGG 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s GC 712s GC 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s GGAG 712s GGAG 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s CTTCGCG 712s CTTCGCG 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s TGCC 712s TGCC 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s AC 712s AC 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s TT 712s TT 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s ACG 712s ACG 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s CGA 712s CGA 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s AGGA 712s AGGA 712s Processing line... 712s GC 712s GC 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s GCGAGGAGGAG 712s GCGAGGAGGAG 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s --- Summary --- 712s Read 1 reference strings 712s Checked 12 alignments, 0 edits 712s --------------- 712s PASSED 712s ALSO checking that bowtie2 and bowtie2-align match up 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 712s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 712s Warning: skipping read '4' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 712s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '12' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 712s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 712s Warning: skipping mate #2 of read '18' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 712s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '27' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 712s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '28' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 712s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '33' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 712s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '50' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 712s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '53' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 712s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '55' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 712s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '58' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 712s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '62' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 712s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '63' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 712s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '64' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 712s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #2 of read '69' because length (1) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '69' because it was < 2 characters long 712s Warning: skipping mate #2 of read '69' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 712s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '70' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 712s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 712s Warning: skipping read '74' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 712s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '75' because it was < 2 characters long 712s Warning: skipping mate #2 of read '75' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 712s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '87' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 712s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '96' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 712s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '97' because it was < 2 characters long 712s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 712s 97 reads; of these: 712s 80 (82.47%) were paired; of these: 712s 79 (98.75%) aligned concordantly 0 times 712s 0 (0.00%) aligned concordantly exactly 1 time 712s 1 (1.25%) aligned concordantly >1 times 712s ---- 712s 79 pairs aligned concordantly 0 times; of these: 712s 0 (0.00%) aligned discordantly 1 time 712s ---- 712s 79 pairs aligned 0 times concordantly or discordantly; of these: 712s 158 mates make up the pairs; of these: 712s 150 (94.94%) aligned 0 times 712s 4 (2.53%) aligned exactly 1 time 712s 4 (2.53%) aligned >1 times 712s 17 (17.53%) were unpaired; of these: 712s 15 (88.24%) aligned 0 times 712s 1 (5.88%) aligned exactly 1 time 712s 1 (5.88%) aligned >1 times 712s 6.78% overall alignment rate 712s /usr/bin/bowtie2 --trim3 3 --score-min L,8.35830530918015,5.22248143419201 --gbar 3 --mm --rfg 47.9976939665172 --cp-min 5 --large-index --n-ceil 1.32340925372661,0.177369486576135 --trim5 9 --cp-ival 1 -q -p 2 -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 712s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 712s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 712s Warning: skipping read '4' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 712s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '12' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 712s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 712s Warning: skipping mate #2 of read '18' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 712s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '27' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 712s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '28' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 712s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '33' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 712s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '50' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 712s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '53' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 712s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '55' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 712s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '58' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 712s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '62' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 712s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '63' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 712s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '64' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 712s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #2 of read '69' because length (1) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '69' because it was < 2 characters long 712s Warning: skipping mate #2 of read '69' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 712s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '70' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 712s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 712s Warning: skipping read '74' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 712s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '75' because it was < 2 characters long 712s Warning: skipping mate #2 of read '75' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 712s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '87' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 712s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '96' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 712s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 712s Warning: skipping mate #1 of read '97' because it was < 2 characters long 712s 97 reads; of these: 712s 80 (82.47%) were paired; of these: 712s 79 (98.75%) aligned concordantly 0 times 712s 0 (0.00%) aligned concordantly exactly 1 time 712s 1 (1.25%) aligned concordantly >1 times 712s ---- 712s 79 pairs aligned concordantly 0 times; of these: 712s 0 (0.00%) aligned discordantly 1 time 712s ---- 712s 79 pairs aligned 0 times concordantly or discordantly; of these: 712s 158 mates make up the pairs; of these: 712s 150 (94.94%) aligned 0 times 712s 4 (2.53%) aligned exactly 1 time 712s 4 (2.53%) aligned >1 times 712s 17 (17.53%) were unpaired; of these: 712s 15 (88.24%) aligned 0 times 712s 1 (5.88%) aligned exactly 1 time 712s 1 (5.88%) aligned >1 times 712s 6.78% overall alignment rate 712s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 712s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 712s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 712s Flattened IUPAC characters 712s Mutating sequence Sim.pm.1 712s Introducing 16 SNPs, 0/1 ref/read gaps, and 1 rearrangements 712s Finished SNPs 712s Finished ref gaps 712s Finished read gaps 712s Mutating sequence Sim.pm.2 712s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 712s Finished SNPs 712s Finished ref gaps 712s Finished read gaps 712s Mutated reference genome to subject genome 712s SNPs introduced: 20 712s Reference gaps introduced: 0 712s Read gaps introduced: 2 712s Rearrangements introduced: 1 712s Created read sampler 712s Sampling 26 reads 712s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 712s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 712s parsing sequence Sim.pm.1... 712s parsing sequence Sim.pm.2... 712s Parsed 40 reference bases 712s *** Run 8 of 100 712s /usr/bin/bowtie2 --cp-ival 1 --local --norc --trim5 8 --large-index --cp-min 5 --mm --rfg 34.4771161752543,13.2461208658853 --rdg 15.0209523941302,5.29239298815532 -R 2 -N 0 -L15 --score-min L,5.12771518894275,3.50512433980385 --trim3 5 --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq 712s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 712s 26 reads; of these: 712s 26 (100.00%) were unpaired; of these: 712s 26 (100.00%) aligned 0 times 712s 0 (0.00%) aligned exactly 1 time 712s 0 (0.00%) aligned >1 times 712s 0.00% overall alignment rate 712s /usr/bin/bowtie2 --cp-ival 1 --local --norc --trim5 8 --large-index --cp-min 5 --mm --rfg 34.4771161752543,13.2461208658853 --rdg 15.0209523941302,5.29239298815532 -R 2 -N 0 -L15 --score-min L,5.12771518894275,3.50512433980385 --trim3 5 --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s --- Summary --- 712s Read 1 reference strings 712s Checked 0 alignments, 0 edits 712s --------------- 712s PASSED 712s ALSO checking that bowtie2 and bowtie2-align match up 712s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 712s 26 reads; of these: 712s 26 (100.00%) were unpaired; of these: 712s 26 (100.00%) aligned 0 times 712s 0 (0.00%) aligned exactly 1 time 712s 0 (0.00%) aligned >1 times 712s 0.00% overall alignment rate 712s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 712s /usr/bin/bowtie2 --cp-ival 1 --local --norc --trim5 8 --large-index --cp-min 5 --mm --rfg 34.4771161752543,13.2461208658853 --rdg 15.0209523941302,5.29239298815532 -R 2 -N 0 -L15 --score-min L,5.12771518894275,3.50512433980385 --trim3 5 --qseq -p 2 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 712s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 712s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 712s 26 reads; of these: 712s 26 (100.00%) were unpaired; of these: 712s 26 (100.00%) aligned 0 times 712s 0 (0.00%) aligned exactly 1 time 712s 0 (0.00%) aligned >1 times 712s 0.00% overall alignment rate 712s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 712s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 712s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 712s /usr/bin/bowtie2 --cp-ival 1 --local --norc --trim5 8 --large-index --cp-min 5 --mm --rfg 34.4771161752543,13.2461208658853 --rdg 15.0209523941302,5.29239298815532 -R 2 -N 0 -L15 --score-min L,5.12771518894275,3.50512433980385 --trim3 5 --qseq -p 3 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 712s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 712s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 712s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 712s 26 reads; of these: 712s 26 (100.00%) were unpaired; of these: 712s 26 (100.00%) aligned 0 times 712s 0 (0.00%) aligned exactly 1 time 712s 0 (0.00%) aligned >1 times 712s 0.00% overall alignment rate 712s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 712s Flattened IUPAC characters 712s Mutating sequence Sim.pm.2 712s Introducing 4 SNPs, 0/1 ref/read gaps, and 1 rearrangements 712s Finished SNPs 712s Finished ref gaps 712s Finished read gaps 712s Mutating sequence Sim.pm.1 712s Introducing 1 SNPs, 2/1 ref/read gaps, and 2 rearrangements 712s Finished SNPs 712s Finished ref gaps 712s Finished read gaps 712s Mutated reference genome to subject genome 712s SNPs introduced: 5 712s Reference gaps introduced: 2 712s Read gaps introduced: 2 712s Rearrangements introduced: 3 712s Created read sampler 712s Sampling 92 reads 712s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 712s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 712s parsing sequence Sim.pm.1... 712s parsing sequence Sim.pm.2... 712s Parsed 40 reference bases 712s *** Run 9 of 100 712s /usr/bin/bowtie2 --rfg 22.749667486512 --mp 7.74648118366064,6.10769400333706 --gbar 2 --trim3 7 --score-min L,9.16588111319574,5.13590850380819 --cp-ival 2 --cp-min 6 --large-index -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta 712s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 712s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '1' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 712s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '2' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 712s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '5' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 712s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '8' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 712s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '12' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 712s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 712s Warning: skipping read '13' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 712s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '18' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 712s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '19' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 712s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 712s Warning: skipping read '25' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 712s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '27' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 712s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '28' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 712s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '29' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 712s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '31' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 712s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '35' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 712s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 712s Warning: skipping read '36' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 712s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '39' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 712s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '44' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 712s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '46' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 712s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '47' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 712s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '50' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 712s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '52' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 712s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '56' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 712s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '61' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 712s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '65' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 712s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '67' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 712s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '74' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 712s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 712s Warning: skipping read '78' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 712s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '79' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 712s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '83' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 712s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '88' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 712s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '91' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 712s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '92' because it was < 2 characters long 712s 92 reads; of these: 712s 92 (100.00%) were unpaired; of these: 712s 91 (98.91%) aligned 0 times 712s 0 (0.00%) aligned exactly 1 time 712s 1 (1.09%) aligned >1 times 712s 1.09% overall alignment rate 712s Read 50 alignments... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s TG 712s TG 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s *** Run 10 of 100 712s /usr/bin/bowtie2 -k 6 -i S,2.55182478712178,4.7198201167326 --mp 7.05108404454875,5.24870312127274 --score-min L,3.02715470795899,7.43233486672326 --ma 24.9483345028052 --nofw --trim3 8 --rfg 8.31532022813439,6.53921152457268 --trim5 0 --norc --large-index --cp-min 3 --cp-ival 2 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s --- Summary --- 712s Read 1 reference strings 712s Checked 1 alignments, 0 edits 712s --------------- 712s PASSED 712s Flattened IUPAC characters 712s Mutating sequence Sim.pm.2 712s Introducing 2 SNPs, 2/0 ref/read gaps, and 1 rearrangements 712s Finished SNPs 712s Finished ref gaps 712s Finished read gaps 712s Mutating sequence Sim.pm.1 712s Introducing 8 SNPs, 0/0 ref/read gaps, and 2 rearrangements 712s Finished SNPs 712s Finished ref gaps 712s Finished read gaps 712s Mutated reference genome to subject genome 712s SNPs introduced: 10 712s Reference gaps introduced: 2 712s Read gaps introduced: 0 712s Rearrangements introduced: 3 712s Created read sampler 712s Sampling 151 reads 712s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 712s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 712s parsing sequence Sim.pm.1... 712s parsing sequence Sim.pm.2... 712s Parsed 40 reference bases 712s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 712s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 712s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '8' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 712s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '12' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 712s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '13' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 712s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '22' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 712s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '31' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 712s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '35' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 712s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 712s Warning: skipping read '38' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 712s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 712s Warning: skipping read '40' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 712s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '45' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 712s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '57' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 712s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '63' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 712s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '65' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 712s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '68' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 712s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '74' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 712s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '78' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 712s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '84' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 712s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '94' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 712s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '95' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 712s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '98' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 712s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '99' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 712s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '106' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 712s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '111' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 712s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '114' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 712s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '119' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 712s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '127' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 712s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '128' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 712s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '136' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 712s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '138' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 712s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '147' because it was < 2 characters long 712s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 712s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 712s Warning: skipping read '151' because length (0) <= # seed mismatches (0) 712s Warning: skipping read '151' because it was < 2 characters long 712s 151 reads; of these: 712s 151 (100.00%) were unpaired; of these: 712s 151 (100.00%) aligned 0 times 712s 0 (0.00%) aligned exactly 1 time 712s 0 (0.00%) aligned >1 times 712s 0.00% overall alignment rate 712s Read 50 alignments... 712s Read 100 alignments... 712s Read 150 alignments... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s Processing line... 712s --- Summary --- 712s Read 1 reference strings 712s Checked 0 alignments, 0 edits 712s --------------- 712s PASSED 712s Flattened IUPAC characters 712s Mutating sequence Sim.pm.2 712s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 712s Finished SNPs 712s Finished ref gaps 712s Finished read gaps 712s Mutating sequence Sim.pm.1 712s Introducing 1 SNPs, 1/3 ref/read gaps, and 0 rearrangements 712s Finished SNPs 712s Finished ref gaps 712s Finished read gaps 712s Mutated reference genome to subject genome 712s SNPs introduced: 11 712s Reference gaps introduced: 1 712s Read gaps introduced: 3 712s Rearrangements introduced: 1 712s Created read sampler 712s Sampling 74 reads 712s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 712s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 712s parsing sequence Sim.pm.1... 712s parsing sequence Sim.pm.2... 712s Parsed 40 reference bases 712s *** Run 11 of 100 712s /usr/bin/bowtie2 --mm --rdg 11.7659615725776,8.98007048447895 -D 38 --score-min L,7.31468524539296,8.2199909429528 --large-index --cp-min 4 --rfg 11.5956440268223,8.03397088166677 --mp 7.08085662865677,3.23373483767149 --trim3 8 --nofw --cp-ival 2 --local -M 5 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '2' because it was < 2 characters long 713s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '3' because it was < 2 characters long 713s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '5' because it was < 2 characters long 713s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '9' because it was < 2 characters long 713s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '11' because it was < 2 characters long 713s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '12' because it was < 2 characters long 713s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '13' because it was < 2 characters long 713s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '15' because it was < 2 characters long 713s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '16' because it was < 2 characters long 713s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '17' because it was < 2 characters long 713s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '18' because it was < 2 characters long 713s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '26' because it was < 2 characters long 713s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '27' because it was < 2 characters long 713s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '33' because it was < 2 characters long 713s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '35' because it was < 2 characters long 713s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '36' because it was < 2 characters long 713s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 713s Warning: skipping read '42' because it was < 2 characters long 713s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '43' because it was < 2 characters long 713s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '44' because it was < 2 characters long 713s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '48' because it was < 2 characters long 713s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '49' because it was < 2 characters long 713s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '60' because it was < 2 characters long 713s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '61' because it was < 2 characters long 713s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '64' because it was < 2 characters long 713s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '65' because it was < 2 characters long 713s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '71' because it was < 2 characters long 713s Warning: skipping read '72' because length (1) <= # seed mismatches (0) 713s Warning: skipping read '72' because it was < 2 characters long 713s 74 reads; of these: 713s 74 (100.00%) were unpaired; of these: 713s 74 (100.00%) aligned 0 times 713s 0 (0.00%) aligned exactly 1 time 713s 0 (0.00%) aligned >1 times 713s 0.00% overall alignment rate 713s Read 50 alignments... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s /usr/bin/bowtie2 --mm --rdg 11.7659615725776,8.98007048447895 -D 38 --score-min L,7.31468524539296,8.2199909429528 --large-index --cp-min 4 --rfg 11.5956440268223,8.03397088166677 --mp 7.08085662865677,3.23373483767149 --trim3 8 --nofw --cp-ival 2 --local -M 5 -q -p 3 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s --- Summary --- 713s Read 1 reference strings 713s Checked 0 alignments, 0 edits 713s --------------- 713s PASSED 713s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '2' because it was < 2 characters long 713s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '3' because it was < 2 characters long 713s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '5' because it was < 2 characters long 713s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '9' because it was < 2 characters long 713s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '11' because it was < 2 characters long 713s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '12' because it was < 2 characters long 713s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '13' because it was < 2 characters long 713s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '15' because it was < 2 characters long 713s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '16' because it was < 2 characters long 713s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '17' because it was < 2 characters long 713s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '18' because it was < 2 characters long 713s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '26' because it was < 2 characters long 713s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '27' because it was < 2 characters long 713s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '33' because it was < 2 characters long 713s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '35' because it was < 2 characters long 713s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '36' because it was < 2 characters long 713s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 713s Warning: skipping read '42' because it was < 2 characters long 713s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '43' because it was < 2 characters long 713s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '44' because it was < 2 characters long 713s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '48' because it was < 2 characters long 713s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '49' because it was < 2 characters long 713s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '60' because it was < 2 characters long 713s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '61' because it was < 2 characters long 713s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '64' because it was < 2 characters long 713s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '65' because it was < 2 characters long 713s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '71' because it was < 2 characters long 713s Warning: skipping read '72' because length (1) <= # seed mismatches (0) 713s Warning: skipping read '72' because it was < 2 characters long 713s 74 reads; of these: 713s 74 (100.00%) were unpaired; of these: 713s 74 (100.00%) aligned 0 times 713s 0 (0.00%) aligned exactly 1 time 713s 0 (0.00%) aligned >1 times 713s 0.00% overall alignment rate 713s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 713s *** Run 12 of 100 713s /usr/bin/bowtie2 --local --cp-ival 1 --cp-min 3 --large-index --score-min L,9.7617964361574,3.48617077307986 -N 1 -L16 --mp 2.31137861752286,1.03775993464961 -r -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.raw -2 /tmp/Sim.pm.qtk7xXsv_2.raw 713s Flattened IUPAC characters 713s Mutating sequence Sim.pm.2 713s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 713s Finished SNPs 713s Finished ref gaps 713s Finished read gaps 713s Mutating sequence Sim.pm.1 713s Introducing 8 SNPs, 1/3 ref/read gaps, and 1 rearrangements 713s Finished SNPs 713s Finished ref gaps 713s Finished read gaps 713s Mutated reference genome to subject genome 713s SNPs introduced: 13 713s Reference gaps introduced: 1 713s Read gaps introduced: 3 713s Rearrangements introduced: 1 713s Created read sampler 713s Sampling 30 reads 713s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 713s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 713s parsing sequence Sim.pm.1... 713s parsing sequence Sim.pm.2... 713s Parsed 40 reference bases 713s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (1) 713s Warning: skipping mate #2 of read '11' because it was < 2 characters long 713s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (1) 713s Warning: skipping mate #1 of read '15' because it was < 2 characters long 713s 30 reads; of these: 713s 30 (100.00%) were paired; of these: 713s 30 (100.00%) aligned concordantly 0 times 713s 0 (0.00%) aligned concordantly exactly 1 time 713s 0 (0.00%) aligned concordantly >1 times 713s ---- 713s 30 pairs aligned concordantly 0 times; of these: 713s 0 (0.00%) aligned discordantly 1 time 713s ---- 713s 30 pairs aligned 0 times concordantly or discordantly; of these: 713s 60 mates make up the pairs; of these: 713s 60 (100.00%) aligned 0 times 713s 0 (0.00%) aligned exactly 1 time 713s 0 (0.00%) aligned >1 times 713s 0.00% overall alignment rate 713s Read 50 alignments... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s --- Summary --- 713s Read 1 reference strings 713s Checked 0 alignments, 0 edits 713s --------------- 713s PASSED 713s *** Run 13 of 100 713s /usr/bin/bowtie2 --large-index --np 2 --cp-min 5 --rdg 1.57954980817704,13.8986717431746 --mm --score-min L,7.6408864494764,4.51581939814829 -R 4 --local --cp-ival 2 --rfg 46.8534432777868,19.1689753375775 -i L,0.274531256563569 -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta 713s Flattened IUPAC characters 713s Mutating sequence Sim.pm.2 713s Introducing 2 SNPs, 3/0 ref/read gaps, and 0 rearrangements 713s Finished SNPs 713s Finished ref gaps 713s Finished read gaps 713s Mutating sequence Sim.pm.1 713s Introducing 11 SNPs, 1/1 ref/read gaps, and 0 rearrangements 713s Finished SNPs 713s Finished ref gaps 713s Finished read gaps 713s Mutated reference genome to subject genome 713s SNPs introduced: 13 713s Reference gaps introduced: 4 713s Read gaps introduced: 1 713s Rearrangements introduced: 0 713s Created read sampler 713s Sampling 47 reads 713s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 713s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 713s parsing sequence Sim.pm.1... 713s parsing sequence Sim.pm.2... 713s Parsed 40 reference bases 713s 47 reads; of these: 713s 47 (100.00%) were unpaired; of these: 713s 47 (100.00%) aligned 0 times 713s 0 (0.00%) aligned exactly 1 time 713s 0 (0.00%) aligned >1 times 713s 0.00% overall alignment rate 713s Read 50 alignments... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s --- Summary --- 713s Read 1 reference strings 713s Checked 0 alignments, 0 edits 713s --------------- 713s PASSED 713s Flattened IUPAC characters 713s Mutating sequence Sim.pm.1 713s Introducing 10 SNPs, 2/0 ref/read gaps, and 1 rearrangements 713s Finished SNPs 713s Finished ref gaps 713s Finished read gaps 713s Mutating sequence Sim.pm.2 713s Introducing 2 SNPs, 1/1 ref/read gaps, and 0 rearrangements 713s Finished SNPs 713s Finished ref gaps 713s Finished read gaps 713s Mutated reference genome to subject genome 713s SNPs introduced: 12 713s Reference gaps introduced: 3 713s Read gaps introduced: 1 713s Rearrangements introduced: 1 713s Created read sampler 713s Sampling 15 reads 713s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 713s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 713s parsing sequence Sim.pm.1... 713s *** Run 14 of 100 713s /usr/bin/bowtie2 --mm --rfg 14.7334622309284 --ma 35.1965384677545 --score-min L,1.35742143512742,8.6559021611473 -R 1 --cp-ival 2 --cp-min 4 -M 8 --large-index --trim5 8 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 713s parsing sequence Sim.pm.2... 713s Parsed 40 reference bases 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 713s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 713s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '3' because it was < 2 characters long 713s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 713s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '5' because it was < 2 characters long 713s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 713s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '8' because it was < 2 characters long 713s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 713s 15 reads; of these: 713s 15 (100.00%) were unpaired; of these: 713s 15 (100.00%) aligned 0 times 713s 0 (0.00%) aligned exactly 1 time 713s 0 (0.00%) aligned >1 times 713s 0.00% overall alignment rate 713s /usr/bin/bowtie2 --mm --rfg 14.7334622309284 --ma 35.1965384677545 --score-min L,1.35742143512742,8.6559021611473 -R 1 --cp-ival 2 --cp-min 4 -M 8 --large-index --trim5 8 -r -p 4 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s --- Summary --- 713s Read 1 reference strings 713s Checked 0 alignments, 0 edits 713s --------------- 713s PASSED 713s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 713s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 713s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '3' because it was < 2 characters long 713s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 713s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '5' because it was < 2 characters long 713s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 713s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 713s Warning: skipping read '8' because it was < 2 characters long 713s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 713s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 713s 15 reads; of these: 713s 15 (100.00%) were unpaired; of these: 713s 15 (100.00%) aligned 0 times 713s 0 (0.00%) aligned exactly 1 time 713s 0 (0.00%) aligned >1 times 713s 0.00% overall alignment rate 713s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 713s Flattened IUPAC characters 713s Mutating sequence Sim.pm.1 713s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 713s Finished SNPs 713s Finished ref gaps 713s Finished read gaps 713s Mutating sequence Sim.pm.2 713s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 713s Finished SNPs 713s Finished ref gaps 713s Finished read gaps 713s Mutated reference genome to subject genome 713s SNPs introduced: 8 713s Reference gaps introduced: 2 713s Read gaps introduced: 0 713s Rearrangements introduced: 0 713s Created read sampler 713s Sampling 109 reads 713s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 713s *** Run 15 of 100 713s /usr/bin/bowtie2 --local --cp-ival 2 --cp-min 4 --large-index --rdg 14.709263849206,19.0358209205069 --score-min L,8.85991742838779,9.57568643611546 -N 0 -L17 --mp 9.2295780519555,3.85761815863547 -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 713s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 713s parsing sequence Sim.pm.1... 713s parsing sequence Sim.pm.2... 713s Parsed 40 reference bases 713s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 713s Warning: skipping mate #1 of read '17' because it was < 2 characters long 713s Read 50 alignments... 713s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 713s Warning: skipping mate #2 of read '52' because it was < 2 characters long 713s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 713s Warning: skipping mate #1 of read '55' because it was < 2 characters long 713s Warning: skipping mate #2 of read '107' because length (1) <= # seed mismatches (0) 713s Warning: skipping mate #2 of read '107' because it was < 2 characters long 713s 109 reads; of these: 713s 109 (100.00%) were paired; of these: 713s 109 (100.00%) aligned concordantly 0 times 713s 0 (0.00%) aligned concordantly exactly 1 time 713s 0 (0.00%) aligned concordantly >1 times 713s ---- 713s 109 pairs aligned concordantly 0 times; of these: 713s 0 (0.00%) aligned discordantly 1 time 713s ---- 713s 109 pairs aligned 0 times concordantly or discordantly; of these: 713s 218 mates make up the pairs; of these: 713s 218 (100.00%) aligned 0 times 713s 0 (0.00%) aligned exactly 1 time 713s 0 (0.00%) aligned >1 times 713s 0.00% overall alignment rate 713s Read 100 alignments... 713s Read 150 alignments... 713s Read 200 alignments... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s /usr/bin/bowtie2 --local --cp-ival 2 --cp-min 4 --large-index --rdg 14.709263849206,19.0358209205069 --score-min L,8.85991742838779,9.57568643611546 -N 0 -L17 --mp 9.2295780519555,3.85761815863547 -f -p 2 -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s Processing line... 713s --- Summary --- 713s Read 1 reference strings 713s Checked 0 alignments, 0 edits 713s --------------- 713s PASSED 713s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 713s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 713s Warning: skipping mate #1 of read '17' because it was < 2 characters long 713s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 713s Warning: skipping mate #2 of read '52' because it was < 2 characters long 713s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 713s Warning: skipping mate #1 of read '55' because it was < 2 characters long 713s Warning: skipping mate #2 of read '107' because length (1) <= # seed mismatches (0) 713s Warning: skipping mate #2 of read '107' because it was < 2 characters long 713s 109 reads; of these: 713s 109 (100.00%) were paired; of these: 713s 109 (100.00%) aligned concordantly 0 times 713s 0 (0.00%) aligned concordantly exactly 1 time 713s 0 (0.00%) aligned concordantly >1 times 713s ---- 713s 109 pairs aligned concordantly 0 times; of these: 713s 0 (0.00%) aligned discordantly 1 time 713s ---- 713s 109 pairs aligned 0 times concordantly or discordantly; of these: 713s 218 mates make up the pairs; of these: 713s 218 (100.00%) aligned 0 times 713s 0 (0.00%) aligned exactly 1 time 713s 0 (0.00%) aligned >1 times 713s 0.00% overall alignment rate 713s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 713s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 713s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 713s Flattened IUPAC characters 713s Mutating sequence Sim.pm.2 713s Introducing 2 SNPs, 0/2 ref/read gaps, and 1 rearrangements 713s Finished SNPs 713s Finished ref gaps 713s Finished read gaps 713s Mutating sequence Sim.pm.1 713s Introducing 5 SNPs, 0/1 ref/read gaps, and 1 rearrangements 713s Finished SNPs 713s Finished ref gaps 713s Finished read gaps 713s Mutated reference genome to subject genome 713s SNPs introduced: 7 713s Reference gaps introduced: 0 713s Read gaps introduced: 3 713s Rearrangements introduced: 2 713s Created read sampler 713s Sampling 84 reads 713s *** Run 16 of 100 713s /usr/bin/bowtie2 --large-index --np 1 --cp-min 4 --score-min L,6.60602510185546,2.48197168995049 --mm --rdg 41.510271137754,4.46770089061678 --trim5 7 -M 4 --cp-ival 2 --local -i S,0.47634734794941 --nofw --rfg 4.45741341304041,9.40894333308571 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 713s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 713s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 713s parsing sequence Sim.pm.1... 713s parsing sequence Sim.pm.2... 713s Parsed 40 reference bases 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 714s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '5' because it was < 2 characters long 714s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '7' because it was < 2 characters long 714s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '9' because it was < 2 characters long 714s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '11' because it was < 2 characters long 714s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '12' because it was < 2 characters long 714s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '15' because it was < 2 characters long 714s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '16' because it was < 2 characters long 714s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '18' because it was < 2 characters long 714s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '19' because it was < 2 characters long 714s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '23' because it was < 2 characters long 714s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '24' because it was < 2 characters long 714s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '26' because it was < 2 characters long 714s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '27' because it was < 2 characters long 714s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '29' because it was < 2 characters long 714s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '47' because it was < 2 characters long 714s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '49' because it was < 2 characters long 714s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '51' because it was < 2 characters long 714s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '55' because it was < 2 characters long 714s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '58' because it was < 2 characters long 714s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '62' because it was < 2 characters long 714s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '64' because it was < 2 characters long 714s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '65' because it was < 2 characters long 714s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '67' because it was < 2 characters long 714s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '72' because it was < 2 characters long 714s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '76' because it was < 2 characters long 714s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '80' because it was < 2 characters long 714s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '81' because it was < 2 characters long 714s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '83' because it was < 2 characters long 714s 84 reads; of these: 714s 84 (100.00%) were unpaired; of these: 714s 84 (100.00%) aligned 0 times 714s 0 (0.00%) aligned exactly 1 time 714s 0 (0.00%) aligned >1 times 714s 0.00% overall alignment rate 714s Read 50 alignments... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s /usr/bin/bowtie2 --large-index --np 1 --cp-min 4 --score-min L,6.60602510185546,2.48197168995049 --mm --rdg 41.510271137754,4.46770089061678 --trim5 7 -M 4 --cp-ival 2 --local -i S,0.47634734794941 --nofw --rfg 4.45741341304041,9.40894333308571 -q -p 3 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s --- Summary --- 714s Read 1 reference strings 714s Checked 0 alignments, 0 edits 714s --------------- 714s PASSED 714s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 714s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 714s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '5' because it was < 2 characters long 714s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '7' because it was < 2 characters long 714s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '9' because it was < 2 characters long 714s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '11' because it was < 2 characters long 714s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '12' because it was < 2 characters long 714s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '15' because it was < 2 characters long 714s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '16' because it was < 2 characters long 714s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '18' because it was < 2 characters long 714s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '19' because it was < 2 characters long 714s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '23' because it was < 2 characters long 714s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '24' because it was < 2 characters long 714s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '26' because it was < 2 characters long 714s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '27' because it was < 2 characters long 714s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '29' because it was < 2 characters long 714s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '47' because it was < 2 characters long 714s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '49' because it was < 2 characters long 714s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '51' because it was < 2 characters long 714s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '55' because it was < 2 characters long 714s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '58' because it was < 2 characters long 714s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '62' because it was < 2 characters long 714s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '64' because it was < 2 characters long 714s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '65' because it was < 2 characters long 714s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '67' because it was < 2 characters long 714s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '72' because it was < 2 characters long 714s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '76' because it was < 2 characters long 714s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '80' because it was < 2 characters long 714s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '81' because it was < 2 characters long 714s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '83' because it was < 2 characters long 714s 84 reads; of these: 714s 84 (100.00%) were unpaired; of these: 714s 84 (100.00%) aligned 0 times 714s 0 (0.00%) aligned exactly 1 time 714s 0 (0.00%) aligned >1 times 714s 0.00% overall alignment rate 714s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 714s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 714s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 714s /usr/bin/bowtie2 --large-index --np 1 --cp-min 4 --score-min L,6.60602510185546,2.48197168995049 --mm --rdg 41.510271137754,4.46770089061678 --trim5 7 -M 4 --cp-ival 2 --local -i S,0.47634734794941 --nofw --rfg 4.45741341304041,9.40894333308571 -q -p 3 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 714s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 714s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 714s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '5' because it was < 2 characters long 714s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '7' because it was < 2 characters long 714s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '9' because it was < 2 characters long 714s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '11' because it was < 2 characters long 714s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '12' because it was < 2 characters long 714s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '15' because it was < 2 characters long 714s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '16' because it was < 2 characters long 714s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '18' because it was < 2 characters long 714s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '19' because it was < 2 characters long 714s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '23' because it was < 2 characters long 714s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '24' because it was < 2 characters long 714s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '26' because it was < 2 characters long 714s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '27' because it was < 2 characters long 714s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '29' because it was < 2 characters long 714s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '47' because it was < 2 characters long 714s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '49' because it was < 2 characters long 714s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '51' because it was < 2 characters long 714s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '55' because it was < 2 characters long 714s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '58' because it was < 2 characters long 714s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '62' because it was < 2 characters long 714s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '64' because it was < 2 characters long 714s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '65' because it was < 2 characters long 714s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '67' because it was < 2 characters long 714s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '72' because it was < 2 characters long 714s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '76' because it was < 2 characters long 714s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '80' because it was < 2 characters long 714s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '81' because it was < 2 characters long 714s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '83' because it was < 2 characters long 714s 84 reads; of these: 714s 84 (100.00%) were unpaired; of these: 714s 84 (100.00%) aligned 0 times 714s 0 (0.00%) aligned exactly 1 time 714s 0 (0.00%) aligned >1 times 714s 0.00% overall alignment rate 714s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 714s Flattened IUPAC characters 714s Mutating sequence Sim.pm.2 714s Introducing 0 SNPs, 1/2 ref/read gaps, and 1 rearrangements 714s Finished SNPs 714s Finished ref gaps 714s Finished read gaps 714s Mutating sequence Sim.pm.1 714s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 714s Finished SNPs 714s Finished ref gaps 714s Finished read gaps 714s Mutated reference genome to subject genome 714s SNPs introduced: 3 714s Reference gaps introduced: 1 714s Read gaps introduced: 2 714s Rearrangements introduced: 1 714s Created read sampler 714s Sampling 77 reads 714s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 714s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 714s parsing sequence Sim.pm.1... 714s parsing sequence Sim.pm.2... 714s Parsed 40 reference bases 714s *** Run 17 of 100 714s /usr/bin/bowtie2 --cp-min 3 --large-index --cp-ival 1 --ma 29.7145392269529 --trim3 8 --score-min L,4.00758096931706,8.10140404040895 -i C,1.14238392659586 --mm --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq 714s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 714s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 714s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 714s Warning: skipping mate #2 of read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 714s Warning: skipping mate #2 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 714s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 714s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 714s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 714s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 714s Warning: skipping mate #2 of read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 714s Warning: skipping mate #2 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 714s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (1) <= # seed mismatches (0) 714s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 714s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 714s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 714s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 714s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 714s Read 50 alignments... 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 714s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 714s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 714s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 714s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 714s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 714s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 714s 77 reads; of these: 714s 63 (81.82%) were paired; of these: 714s 63 (100.00%) aligned concordantly 0 times 714s 0 (0.00%) aligned concordantly exactly 1 time 714s 0 (0.00%) aligned concordantly >1 times 714s ---- 714s 63 pairs aligned concordantly 0 times; of these: 714s 0 (0.00%) aligned discordantly 1 time 714s ---- 714s 63 pairs aligned 0 times concordantly or discordantly; of these: 714s 126 mates make up the pairs; of these: 714s 124 (98.41%) aligned 0 times 714s 1 (0.79%) aligned exactly 1 time 714s 1 (0.79%) aligned >1 times 714s 14 (18.18%) were unpaired; of these: 714s 14 (100.00%) aligned 0 times 714s 0 (0.00%) aligned exactly 1 time 714s 0 (0.00%) aligned >1 times 714s 1.43% overall alignment rate 714s Read 100 alignments... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s GGAGGAG 714s GGAGGAG 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s GA 714s GA 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s --- Summary --- 714s Read 1 reference strings 714s Checked 2 alignments, 0 edits 714s --------------- 714s PASSED 714s Flattened IUPAC characters 714s Mutating sequence Sim.pm.1 714s Introducing 9 SNPs, 0/2 ref/read gaps, and 0 rearrangements 714s Finished SNPs 714s Finished ref gaps 714s Finished read gaps 714s Mutating sequence Sim.pm.2 714s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 714s Finished SNPs 714s Finished ref gaps 714s Finished read gaps 714s Mutated reference genome to subject genome 714s SNPs introduced: 10 714s Reference gaps introduced: 0 714s Read gaps introduced: 2 714s Rearrangements introduced: 0 714s Created read sampler 714s Sampling 129 reads 714s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 714s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 714s parsing sequence Sim.pm.1... 714s parsing sequence Sim.pm.2... 714s Parsed 40 reference bases 714s *** Run 18 of 100 714s /usr/bin/bowtie2 --mp 4.75069699753506,3.8011731883044 -N 0 -L22 --nofw --score-min L,1.9717331545415,8.77698106227601 --cp-ival 2 --local --cp-min 2 -a --large-index -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 714s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 714s Warning: skipping mate #2 of read '82' because it was < 2 characters long 714s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 714s Warning: skipping mate #1 of read '85' because it was < 2 characters long 714s Read 50 alignments... 714s Read 100 alignments... 714s *** Run 19 of 100 714s /usr/bin/bowtie2 --mm --rdg 28.8237668923196 -R 3 --score-min L,4.13800220178915,8.65773704364321 --large-index --np 1 --cp-min 8 --rfg 17.342336480086,4.17614399966422 --mp 4.92842397508958,4.0334805105095 --cp-ival 1 --local --trim5 5 --n-ceil 1.19409202481519,0.66354061123028 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 714s Warning: skipping mate #1 of read '110' because length (1) <= # seed mismatches (0) 714s Warning: skipping mate #1 of read '110' because it was < 2 characters long 714s 129 Read 150 alignments... 714s reads; of these: 714s 129 (100.00%) were paired; of these: 714s 129 (100.00%) aligned concordantly 0 times 714s 0 (0.00%) aligned concordantly exactly 1 time 714s 0 (0.00%) aligned concordantly >1 times 714s ---- 714s 129 pairs aligned concordantly 0 times; of these: 714s 0 (0.00%) aligned discordantly 1 time 714s ---- 714s 129 pairs aligned 0 times concordantly or discordantly; of these: 714s 258 mates make up the pairs; of these: 714s 258 (100.00%) aligned 0 times 714s 0 (0.00%) aligned exactly 1 time 714s 0 (0.00%) aligned >1 times 714s 0.00% overall alignment rate 714s Read 200 alignments... 714s Read 250 alignments... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s --- Summary --- 714s Read 1 reference strings 714s Checked 0 alignments, 0 edits 714s --------------- 714s PASSED 714s Flattened IUPAC characters 714s Mutating sequence Sim.pm.2 714s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 714s Finished SNPs 714s Finished ref gaps 714s Finished read gaps 714s Mutating sequence Sim.pm.1 714s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 714s Finished SNPs 714s Finished ref gaps 714s Finished read gaps 714s Mutated reference genome to subject genome 714s SNPs introduced: 7 714s Reference gaps introduced: 0 714s Read gaps introduced: 1 714s Rearrangements introduced: 0 714s Created read sampler 714s Sampling 52 reads 714s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 714s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 714s parsing sequence Sim.pm.1... 714s parsing sequence Sim.pm.2... 714s Parsed 40 reference bases 714s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '5' because it was < 2 characters long 714s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '6' because it was < 2 characters long 714s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '17' because it was < 2 characters long 714s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '20' because it was < 2 characters long 714s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '27' because it was < 2 characters long 714s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '50' because it was < 2 characters long 714s 52 reads; of these: 714s 52 (100.00%) were unpaired; of these: 714s 52 (100.00%) aligned 0 times 714s 0 (0.00%) aligned exactly 1 time 714s 0 (0.00%) aligned >1 times 714s 0.00% overall alignment rate 714s Read 50 alignments... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s /usr/bin/bowtie2 --mm --rdg 28.8237668923196 -R 3 --score-min L,4.13800220178915,8.65773704364321 --large-index --np 1 --cp-min 8 --rfg 17.342336480086,4.17614399966422 --mp 4.92842397508958,4.0334805105095 --cp-ival 1 --local --trim5 5 --n-ceil 1.19409202481519,0.66354061123028 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s --- Summary --- 714s Read 1 reference strings 714s Checked 0 alignments, 0 edits 714s --------------- 714s PASSED 714s ALSO checking that bowtie2 and bowtie2-align match up 714s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '5' because it was < 2 characters long 714s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 714s Warning: skipping read '6' because it was < 2 characters long 714s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '17' because it was < 2 characters long 714s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '20' because it was < 2 characters long 714s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '27' because it was < 2 characters long 714s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 714s Warning: skipping read '50' because it was < 2 characters long 714s 52 reads; of these: 714s 52 (100.00%) were unpaired; of these: 714s 52 (100.00%) aligned 0 times 714s 0 (0.00%) aligned exactly 1 time 714s 0 (0.00%) aligned >1 times 714s 0.00% overall alignment rate 714s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 714s Flattened IUPAC characters 714s Mutating sequence Sim.pm.2 714s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 714s Finished SNPs 714s Finished ref gaps 714s Finished read gaps 714s Mutating sequence Sim.pm.1 714s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 714s Finished SNPs 714s Finished ref gaps 714s Finished read gaps 714s Mutated reference genome to subject genome 714s SNPs introduced: 8 714s Reference gaps introduced: 0 714s Read gaps introduced: 0 714s Rearrangements introduced: 1 714s Created read sampler 714s Sampling 68 reads 714s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 714s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 714s parsing sequence Sim.pm.1... 714s parsing sequence Sim.pm.2... 714s *** Run 20 of 100 714s /usr/bin/bowtie2 --large-index --np 2 --cp-min 2 --cp-ival 4 --score-min L,7.95020623168327,7.8542240404566 --nofw -N 0 -L26 --rdg 43.6021426921627 --rfg 12.0803905789895 -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq 714s Parsed 40 reference bases 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 714s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 714s Warning: skipping mate #2 of read '7' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 714s Warning: skipping mate #1 of read '26' because length (1) <= # seed mismatches (0) 714s Warning: skipping mate #1 of read '26' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 714s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 714s Warning: skipping mate #2 of read '61' because it was < 2 characters long 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 714s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 714s Read 50 alignments... 714s 68 reads; of these: 714s 68 (100.00%) were paired; of these: 714s 68 (100.00%) aligned concordantly 0 times 714s 0 (0.00%) aligned concordantly exactly 1 time 714s 0 (0.00%) aligned concordantly >1 times 714s ---- 714s 68 pairs aligned concordantly 0 times; of these: 714s 0 (0.00%) aligned discordantly 1 time 714s ---- 714s 68 pairs aligned 0 times concordantly or discordantly; of these: 714s 136 mates make up the pairs; of these: 714s 124 (91.18%) aligned 0 times 714s 5 (3.68%) aligned exactly 1 time 714s 7 (5.15%) aligned >1 times 714s 8.82% overall alignment rate 714s Read 100 alignments... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s CG 714s CG 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s GA 714s GA 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s GC 714s GC 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s Processing line... 714s TGCCGG 714s TGCCGG 714s Processing line... 715s /usr/bin/bowtie2 --large-index --np 2 --cp-min 2 --cp-ival 4 --score-min L,7.95020623168327,7.8542240404566 --nofw -N 0 -L26 --rdg 43.6021426921627 --rfg 12.0803905789895 -q -p 4 -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s GGG 715s GGG 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s TGCGC 715s TGCGC 715s Processing line... 715s Processing line... 715s GCG 715s GCG 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s AG 715s AG 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s CTG 715s CTG 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s TCTTCGCGAGGAG 715s TCTTCGCGAGGAG 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s TCTTC 715s TCTTC 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s GAGG 715s GAGG 715s Processing line... 715s Processing line... 715s Processing line... 715s --- Summary --- 715s Read 1 reference strings 715s Checked 12 alignments, 0 edits 715s --------------- 715s PASSED 715s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 715s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #2 of read '7' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 715s Warning: skipping mate #1 of read '26' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #1 of read '26' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 715s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #2 of read '61' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 715s 68 reads; of these: 715s 68 (100.00%) were paired; of these: 715s 68 (100.00%) aligned concordantly 0 times 715s 0 (0.00%) aligned concordantly exactly 1 time 715s 0 (0.00%) aligned concordantly >1 times 715s ---- 715s 68 pairs aligned concordantly 0 times; of these: 715s 0 (0.00%) aligned discordantly 1 time 715s ---- 715s 68 pairs aligned 0 times concordantly or discordantly; of these: 715s 136 mates make up the pairs; of these: 715s 124 (91.18%) aligned 0 times 715s 5 (3.68%) aligned exactly 1 time 715s 7 (5.15%) aligned >1 times 715s 8.82% overall alignment rate 715s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 715s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 715s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 715s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 715s /usr/bin/bowtie2 --large-index --np 2 --cp-min 2 --cp-ival 4 --score-min L,7.95020623168327,7.8542240404566 --nofw -N 0 -L26 --rdg 43.6021426921627 --rfg 12.0803905789895 -q -p 3 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 715s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #2 of read '7' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 715s Warning: skipping mate #1 of read '26' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #1 of read '26' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 715s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #2 of read '61' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 715s 68 reads; of these: 715s 68 (100.00%) were paired; of these: 715s 68 (100.00%) aligned concordantly 0 times 715s 0 (0.00%) aligned concordantly exactly 1 time 715s 0 (0.00%) aligned concordantly >1 times 715s ---- 715s 68 pairs aligned concordantly 0 times; of these: 715s 0 (0.00%) aligned discordantly 1 time 715s ---- 715s 68 pairs aligned 0 times concordantly or discordantly; of these: 715s 136 mates make up the pairs; of these: 715s 124 (91.18%) aligned 0 times 715s 5 (3.68%) aligned exactly 1 time 715s 7 (5.15%) aligned >1 times 715s 8.82% overall alignment rate 715s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 715s Flattened IUPAC characters 715s Mutating sequence Sim.pm.1 715s Introducing 12 SNPs, 1/0 ref/read gaps, and 1 rearrangements 715s Finished SNPs 715s Finished ref gaps 715s Finished read gaps 715s Mutating sequence Sim.pm.2 715s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 715s Finished SNPs 715s Finished ref gaps 715s Finished read gaps 715s Mutated reference genome to subject genome 715s SNPs introduced: 20 715s Reference gaps introduced: 1 715s Read gaps introduced: 0 715s Rearrangements introduced: 2 715s Created read sampler 715s Sampling 147 reads 715s *** Run 21 of 100 715s /usr/bin/bowtie2 --cp-min 4 --large-index --gbar 4 -k 9 --ma 9.13420174662357 --score-min L,8.90535016169528,7.39975947047563 --mm --rdg 8.36288420196863 --cp-ival 1 --mp 8.9237308881791,5.55342415116777 --trim3 1 --rfg 43.828966945625,3.68838869617928 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 715s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 715s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 715s parsing sequence Sim.pm.1... 715s parsing sequence Sim.pm.2... 715s Parsed 40 reference bases 715s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 715s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 715s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 715s Warning: skipping read '14' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 715s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 715s Warning: skipping read '19' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 715s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 715s Warning: skipping read '60' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 715s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 715s Warning: skipping read '74' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 715s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 715s Warning: skipping read '95' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 715s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 715s Warning: skipping read '104' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 715s Read 50 alignments... 715s Read 100 alignments... 715s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 715s Warning: skipping read '145' because length (1) <= # seed mismatches (0) 715s Warning: skipping read '145' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 715s 147 reads; of these: 715s 147 (100.00%) were unpaired; of these: 715s 133 (90.48%) aligned 0 times 715s 3 (2.04%) aligned exactly 1 time 715s 11 (7.48%) aligned >1 times 715s 9.52% overall alignment rate 715s Read 150 alignments... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s GA 715s GA 715s Processing line... 715s GA 715s GA 715s Processing line... 715s TC 715s TC 715s Processing line... 715s GA 715s GA 715s Processing line... 715s GA 715s GA 715s Processing line... 715s TC 715s TC 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s GA 715s GA 715s Processing line... 715s TC 715s TC 715s Processing line... 715s TC 715s TC 715s Processing line... 715s GA 715s GA 715s Processing line... 715s GA 715s GA 715s Processing line... 715s GA 715s GA 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s TG 715s TG 715s Processing line... 715s CA 715s CA 715s Processing line... 715s TG 715s TG 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s GA 715s GA 715s Processing line... 715s TC 715s TC 715s Processing line... 715s TC 715s TC 715s Processing line... 715s GA 715s GA 715s Processing line... 715s GA 715s GA 715s Processing line... 715s GA 715s GA 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s GCC 715s GCC 715s Processing line... 715s GCC 715s GCC 715s Processing line... 715s GGC 715s GGC 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s GGG 715s GGG 715s Processing line... 715s GGG 715s GGG 715s Processing line... 715s GGG 715s GGG 715s Processing line... 715s Processing line... 715s AG 715s AG 715s Processing line... 715s CT 715s CT 715s Processing line... 715s AG 715s AG 715s Processing line... 715s AG 715s AG 715s Processing line... 715s CT 715s CT 715s Processing line... 715s Processing line... 715s Processing line... 715s CGA 715s CGA 715s Processing line... 715s TCG 715s TCG 715s Processing line... 715s CGA 715s CGA 715s Processing line... 715s Processing line... 715s CGAGGAGGA 715s CGAGGAGGA 715s Processing line... 715s CGGGGG 715s CGGGGG 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s AC 715s AC 715s Processing line... 715s AC 715s AC 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s GGA 715s GGA 715s Processing line... 715s GGA 715s GGA 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s TGCGCGACG 715s TGCGCGACG 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s AC 715s AC 715s Processing line... 715s AC 715s AC 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s --- Summary --- 715s Read 1 reference strings 715s Checked 44 alignments, 0 edits 715s --------------- 715s PASSED 715s Flattened IUPAC characters 715s Mutating sequence Sim.pm.2 715s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 715s Finished SNPs 715s Finished ref gaps 715s Finished read gaps 715s Mutating sequence Sim.pm.1 715s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 715s Finished SNPs 715s Finished ref gaps 715s Finished read gaps 715s Mutated reference genome to subject genome 715s SNPs introduced: 3 715s Reference gaps introduced: 1 715s Read gaps introduced: 0 715s Rearrangements introduced: 1 715s Created read sampler 715s Sampling 94 reads 715s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 715s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 715s parsing sequence Sim.pm.1... 715s parsing sequence Sim.pm.2... 715s Parsed 40 reference bases 715s *** Run 22 of 100 715s /usr/bin/bowtie2 --score-min L,2.45925285063521,3.00541050381022 --mm -a --large-index --np 7 --cp-min 5 --n-ceil 1.28820727835298,0.374867675064016 --cp-ival 1 --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 715s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 715s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 715s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 715s Read 50 alignments... 715s Read 100 alignments... 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 715s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 715s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 715s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 715s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 715s Warning: skipping mate #2 of read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #2 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 715s 94 reads; of these: 715s 94 (100.00%) were paired; of these: 715s 93 (98.94%) aligned concordantly 0 times 715s 0 (0.00%) aligned concordantly exactly 1 time 715s 1 (1.06%) aligned concordantly >1 times 715s ---- 715s 93 pairs aligned concordantly 0 times; of these: 715s 0 (0.00%) aligned discordantly 1 time 715s ---- 715s 93 pairs aligned 0 times concordantly or discordantly; of these: 715s 186 mates make up the pairs; of these: 715s 177 (95.16%) aligned 0 times 715s 4 (2.15%) aligned exactly 1 time 715s 5 (2.69%) aligned >1 times 715s 5.85% overall alignment rate 715s Read 150 alignments... 715s Read 200 alignments... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s TCTTCGCGAGGAGGA 715s TCTTCGCGAGGAGGA 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s CG 715s CG 715s Processing line... 715s CG 715s CG 715s Processing line... 715s CG 715s CG 715s Processing line... 715s CG 715s CG 715s Processing line... 715s CG 715s CG 715s Processing line... 715s CG 715s CG 715s Processing line... 715s CG 715s CG 715s Processing line... 715s CG 715s CG 715s Processing line... 715s CG 715s CG 715s Processing line... 715s CG 715s CG 715s Processing line... 715s CG 715s CG 715s Processing line... 715s CG 715s CG 715s Processing line... 715s Processing line... 715s ATCT 715s ATCT 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s TGC 715s TGC 715s Processing line... 715s AC 715s AC 715s Processing line... 715s TGC 715s TGC 715s Processing line... 715s AC 715s AC 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s /usr/bin/bowtie2 --score-min L,2.45925285063521,3.00541050381022 --mm -a --large-index --np 7 --cp-min 5 --n-ceil 1.28820727835298,0.374867675064016 --cp-ival 1 --qseq -p 4 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s TT 715s TT 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s GA 715s GA 715s Processing line... 715s GA 715s GA 715s Processing line... 715s GA 715s GA 715s Processing line... 715s TC 715s TC 715s Processing line... 715s TC 715s TC 715s Processing line... 715s GA 715s GA 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s CGAGGAGGAG 715s CGAGGAGGAG 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s CA 715s CA 715s Processing line... 715s TG 715s TG 715s Processing line... 715s TG 715s TG 715s Processing line... 715s Processing line... 715s CA 715s CA 715s Processing line... 715s TG 715s TG 715s Processing line... 715s TG 715s TG 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s GAG 715s GAG 715s Processing line... 715s GAG 715s GAG 715s Processing line... 715s GAG 715s GAG 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s --- Summary --- 715s Read 1 reference strings 715s Checked 35 alignments, 0 edits 715s --------------- 715s PASSED 715s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 715s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 715s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 715s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 715s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 715s Warning: skipping mate #2 of read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #2 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 715s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 715s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 715s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 715s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 715s 94 reads; of these: 715s 94 (100.00%) were paired; of these: 715s 93 (98.94%) aligned concordantly 0 times 715s 0 (0.00%) aligned concordantly exactly 1 time 715s 1 (1.06%) aligned concordantly >1 times 715s ---- 715s 93 pairs aligned concordantly 0 times; of these: 715s 0 (0.00%) aligned discordantly 1 time 715s ---- 715s 93 pairs aligned 0 times concordantly or discordantly; of these: 715s 186 mates make up the pairs; of these: 715s 177 (95.16%) aligned 0 times 715s 4 (2.15%) aligned exactly 1 time 715s 5 (2.69%) aligned >1 times 715s 5.85% overall alignment rate 715s Flattened IUPAC characters 715s Mutating sequence Sim.pm.1 715s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 715s Finished SNPs 715s Finished ref gaps 715s Finished read gaps 715s Mutating sequence Sim.pm.2 715s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 715s Finished SNPs 715s Finished ref gaps 715s Finished read gaps 715s Mutated reference genome to subject genome 715s SNPs introduced: 9 715s Reference gaps introduced: 0 715s Read gaps introduced: 0 715s Rearrangements introduced: 1 715s Created read sampler 715s Sampling 18 reads 715s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 715s *** Run 23 of 100 715s /usr/bin/bowtie2 --large-index --cp-min 5 --norc --cp-ival 1 --score-min L,8.36717012767189,5.07924839096894 --nofw --gbar 5 -D 2 --rdg 1.65341008712531 --rfg 35.2059741991143,16.4869495622771 --mm --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq 715s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 715s parsing sequence Sim.pm.1... 715s parsing sequence Sim.pm.2... 715s Parsed 40 reference bases 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 715s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 715s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 715s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 715s 18 reads; of these: 715s 18 (100.00%) were paired; of these: 715s 18 (100.00%) aligned concordantly 0 times 715s 0 (0.00%) aligned concordantly exactly 1 time 715s 0 (0.00%) aligned concordantly >1 times 715s ---- 715s 18 pairs aligned concordantly 0 times; of these: 715s 0 (0.00%) aligned discordantly 1 time 715s ---- 715s 18 pairs aligned 0 times concordantly or discordantly; of these: 715s 36 mates make up the pairs; of these: 715s 36 (100.00%) aligned 0 times 715s 0 (0.00%) aligned exactly 1 time 715s 0 (0.00%) aligned >1 times 715s 0.00% overall alignment rate 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s /usr/bin/bowtie2 --large-index --cp-min 5 --norc --cp-ival 1 --score-min L,8.36717012767189,5.07924839096894 --nofw --gbar 5 -D 2 --rdg 1.65341008712531 --rfg 35.2059741991143,16.4869495622771 --mm --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s Processing line... 715s --- Summary --- 715s Read 1 reference strings 715s Checked 0 alignments, 0 edits 715s --------------- 715s PASSED 715s ALSO checking that bowtie2 and bowtie2-align match up 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 716s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 716s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 716s 18 reads; of these: 716s 18 (100.00%) were paired; of these: 716s 18 (100.00%) aligned concordantly 0 times 716s 0 (0.00%) aligned concordantly exactly 1 time 716s 0 (0.00%) aligned concordantly >1 times 716s ---- 716s 18 pairs aligned concordantly 0 times; of these: 716s 0 (0.00%) aligned discordantly 1 time 716s ---- 716s 18 pairs aligned 0 times concordantly or discordantly; of these: 716s 36 mates make up the pairs; of these: 716s 36 (100.00%) aligned 0 times 716s 0 (0.00%) aligned exactly 1 time 716s 0 (0.00%) aligned >1 times 716s 0.00% overall alignment rate 716s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 716s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 716s /usr/bin/bowtie2 --large-index --cp-min 5 --norc --cp-ival 1 --score-min L,8.36717012767189,5.07924839096894 --nofw --gbar 5 -D 2 --rdg 1.65341008712531 --rfg 35.2059741991143,16.4869495622771 --mm --qseq -p 4 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 716s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 716s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 716s 18 reads; of these: 716s 18 (100.00%) were paired; of these: 716s 18 (100.00%) aligned concordantly 0 times 716s 0 (0.00%) aligned concordantly exactly 1 time 716s 0 (0.00%) aligned concordantly >1 times 716s ---- 716s 18 pairs aligned concordantly 0 times; of these: 716s 0 (0.00%) aligned discordantly 1 time 716s ---- 716s 18 pairs aligned 0 times concordantly or discordantly; of these: 716s 36 mates make up the pairs; of these: 716s 36 (100.00%) aligned 0 times 716s 0 (0.00%) aligned exactly 1 time 716s 0 (0.00%) aligned >1 times 716s 0.00% overall alignment rate 716s Flattened IUPAC characters 716s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 716s Mutating sequence Sim.pm.2 716s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 716s Finished SNPs 716s Finished ref gaps 716s Finished read gaps 716s Mutating sequence Sim.pm.1 716s Introducing 3 SNPs, 3/1 ref/read gaps, and 0 rearrangements 716s Finished SNPs 716s Finished ref gaps 716s Finished read gaps 716s Mutated reference genome to subject genome 716s SNPs introduced: 7 716s Reference gaps introduced: 3 716s Read gaps introduced: 2 716s Rearrangements introduced: 0 716s Created read sampler 716s Sampling 64 reads 716s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 716s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 716s parsing sequence Sim.pm.1... 716s parsing sequence Sim.pm.2... 716s Parsed 40 reference bases 716s *** Run 24 of 100 716s /usr/bin/bowtie2 --local --cp-ival 1 --large-index --np 27 --cp-min 3 --rfg 20.4166997575292,5.45197281633396 --score-min L,1.52614416541637,4.69398976582528 -R 2 -i C,3.46591749908542 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 716s 64 reads; of these: 716s 64 (100.00%) were unpaired; of these: 716s 64 (100.00%) aligned 0 times 716s 0 (0.00%) aligned exactly 1 time 716s 0 (0.00%) aligned >1 times 716s 0.00% overall alignment rate 716s Read 50 alignments... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s --- Summary --- 716s Read 1 reference strings 716s Checked 0 alignments, 0 edits 716s --------------- 716s PASSED 716s Flattened IUPAC characters 716s Mutating sequence Sim.pm.2 716s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 716s Finished SNPs 716s Finished ref gaps 716s Finished read gaps 716s Mutating sequence Sim.pm.1 716s Introducing 17 SNPs, 0/1 ref/read gaps, and 3 rearrangements 716s Finished SNPs 716s Finished ref gaps 716s *** Run 25 of 100 716s /usr/bin/bowtie2 --rfg 27.5188293820715 --score-min L,2.52366587636601,5.9506722385097 --trim3 0 --ma 10.6867019298345 -N 0 -L27 --cp-ival 2 --large-index --cp-min 3 --np 4 --n-ceil 1.39097135641266,0.170254641199319 --norc -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 716s Finished read gaps 716s Mutated reference genome to subject genome 716s SNPs introduced: 24 716s Reference gaps introduced: 0 716s Read gaps introduced: 1 716s Rearrangements introduced: 3 716s Created read sampler 716s Sampling 105 reads 716s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 716s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 716s parsing sequence Sim.pm.1... 716s parsing sequence Sim.pm.2... 716s Parsed 40 reference bases 716s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 716s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 716s 105 reads; of these: 716s 105 (100.00%) were unpaired; of these: 716s 99 (94.29%) aligned 0 times 716s 2 (1.90%) aligned exactly 1 time 716s 4 (3.81%) aligned >1 times 716s 5.71% overall alignment rate 716s Read 50 alignments... 716s Read 100 alignments... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s CC 716s CC 716s Processing line... 716s TCT 716s TCT 716s Processing line... 716s CTTCGCGAG 716s CTTCGCGAG 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s CGC 716s CGC 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s GC 716s GC 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s AC 716s AC 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s --- Summary --- 716s Read 1 reference strings 716s Checked 6 alignments, 0 edits 716s --------------- 716s PASSED 716s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 716s /usr/bin/bowtie2 --rfg 27.5188293820715 --score-min L,2.52366587636601,5.9506722385097 --trim3 0 --ma 10.6867019298345 -N 0 -L27 --cp-ival 2 --large-index --cp-min 3 --np 4 --n-ceil 1.39097135641266,0.170254641199319 --norc -r -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 716s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 716s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 716s 105 reads; of these: 716s 105 (100.00%) were unpaired; of these: 716s 99 (94.29%) aligned 0 times 716s 2 (1.90%) aligned exactly 1 time 716s 4 (3.81%) aligned >1 times 716s 5.71% overall alignment rate 716s Flattened IUPAC characters 716s Mutating sequence Sim.pm.2 716s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 716s Finished SNPs 716s Finished ref gaps 716s Finished read gaps 716s Mutating sequence Sim.pm.1 716s Introducing 9 SNPs, 0/0 ref/read gaps, and 1 rearrangements 716s Finished SNPs 716s Finished ref gaps 716s Finished read gaps 716s Mutated reference genome to subject genome 716s SNPs introduced: 16 716s Reference gaps introduced: 0 716s Read gaps introduced: 0 716s Rearrangements introduced: 1 716s Created read sampler 716s Sampling 38 reads 716s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 716s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 716s parsing sequence Sim.pm.1... 716s parsing sequence Sim.pm.2... 716s Parsed 40 reference bases 716s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 716s *** Run 26 of 100 716s /usr/bin/bowtie2 --score-min L,1.94706132751899,1.71658699769056 --trim3 5 --mp 7.89267375128217,7.66912010771931 -R 4 --rfg 10.9744427818002 --large-index --np 1 --cp-min 2 --trim5 5 --norc --cp-ival 2 -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 716s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 716s Warning: skipping mate #2 of read '2' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 716s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 716s Warning: skipping mate #1 of read '3' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 716s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 716s Warning: skipping mate #1 of read '10' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 716s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 716s Warning: skipping mate #1 of read '11' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 716s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '13' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 716s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 716s Warning: skipping mate #1 of read '14' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 716s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 716s Warning: skipping mate #1 of read '25' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 716s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 716s Warning: skipping mate #1 of read '26' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 716s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 716s Warning: skipping mate #1 of read '27' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 716s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '28' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 716s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 716s Warning: skipping mate #1 of read '30' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 716s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 716s Warning: skipping mate #1 of read '35' because it was < 2 characters long 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 716s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 716s 38 reads; of these: 716s 32 (84.21%) were paired; of these: 716s 32 (100.00%) aligned concordantly 0 times 716s 0 (0.00%) aligned concordantly exactly 1 time 716s 0 (0.00%) aligned concordantly >1 times 716s ---- 716s 32 pairs aligned concordantly 0 times; of these: 716s 0 (0.00%) aligned discordantly 1 time 716s ---- 716s 32 pairs aligned 0 times concordantly or discordantly; of these: 716s 64 mates make up the pairs; of these: 716s 62 (96.88%) aligned 0 times 716s 1 (1.56%) aligned exactly 1 time 716s 1 (1.56%) aligned >1 times 716s 6 (15.79%) were unpaired; of these: 716s 6 (100.00%) aligned 0 times 716s 0 (0.00%) aligned exactly 1 time 716s 0 (0.00%) aligned >1 times 716s 2.86% overall alignment rate 716s Read 50 alignments... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s GG 716s GG 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s TTCG 716s TTCG 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s --- Summary --- 716s Read 1 reference strings 716s Checked 2 alignments, 0 edits 716s --------------- 716s PASSED 716s Flattened IUPAC characters 716s Mutating sequence Sim.pm.2 716s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 716s Finished SNPs 716s Finished ref gaps 716s Finished read gaps 716s Mutating sequence Sim.pm.1 716s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 716s Finished SNPs 716s Finished ref gaps 716s Finished read gaps 716s Mutated reference genome to subject genome 716s SNPs introduced: 11 716s Reference gaps introduced: 0 716s Read gaps introduced: 0 716s Rearrangements introduced: 0 716s Created read sampler 716s Sampling 76 reads 716s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 716s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 716s parsing sequence Sim.pm.1... 716s parsing sequence Sim.pm.2... 716s Parsed 40 reference bases 716s *** Run 27 of 100 716s /usr/bin/bowtie2 --rdg 49.5016007454303 --rfg 35.9033499326486 --trim3 8 --score-min L,8.36055737158627,8.91786859325079 -R 3 -i S -N 0 -L26 --local --cp-ival 2 --cp-min 5 --large-index -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 716s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 716s Warning: skipping read '4' because it was < 2 characters long 716s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '6' because it was < 2 characters long 716s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '7' because it was < 2 characters long 716s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '10' because it was < 2 characters long 716s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 716s Warning: skipping read '17' because it was < 2 characters long 716s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '24' because it was < 2 characters long 716s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '25' because it was < 2 characters long 716s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '27' because it was < 2 characters long 716s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '38' because it was < 2 characters long 716s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '45' because it was < 2 characters long 716s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '53' because it was < 2 characters long 716s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '54' because it was < 2 characters long 716s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '55' because it was < 2 characters long 716s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '65' because it was < 2 characters long 716s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '68' because it was < 2 characters long 716s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '70' because it was < 2 characters long 716s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '72' because it was < 2 characters long 716s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '73' because it was < 2 characters long 716s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 716s Warning: skipping read '75' because it was < 2 characters long 716s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 716s Warning: skipping read '76' because it was < 2 characters long 716s 76 reads; of these: 716s 76 (100.00%) were unpaired; of these: 716s 76 (100.00%) aligned 0 times 716s 0 (0.00%) aligned exactly 1 time 716s 0 (0.00%) aligned >1 times 716s 0.00% overall alignment rate 716s Read 50 alignments... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s Processing line... 716s --- Summary --- 716s Read 1 reference strings 716s Checked 0 alignments, 0 edits 716s --------------- 716s PASSED 716s Flattened IUPAC characters 716s Mutating sequence Sim.pm.2 716s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 716s Finished SNPs 716s Finished ref gaps 716s Finished read gaps 716s Mutating sequence Sim.pm.1 716s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 716s Finished SNPs 716s Finished ref gaps 716s Finished read gaps 716s Mutated reference genome to subject genome 716s SNPs introduced: 6 716s Reference gaps introduced: 0 716s Read gaps introduced: 2 716s Rearrangements introduced: 0 716s Created read sampler 716s Sampling 129 reads 716s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 716s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 716s parsing sequence Sim.pm.1... 716s parsing sequence Sim.pm.2... 716s Parsed 40 reference bases 716s *** Run 28 of 100 716s /usr/bin/bowtie2 --score-min L,1.90435436408507,5.10840805676518 --trim3 5 --ma 14.5469728514984 -k 2 --mp 5.2363742255102,4.7330180333492 --large-index --np 3 --cp-min 4 --cp-ival 3 --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq 716s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 717s 129 reads; of these: 717s 129 (100.00%) were unpaired; of these: 717s 125 (96.90%) aligned 0 times 717s 2 (1.55%) aligned exactly 1 time 717s 2 (1.55%) aligned >1 times 717s 3.10% overall alignment rate 717s Read 50 alignments... 717s Read 100 alignments... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s /usr/bin/bowtie2 --score-min L,1.90435436408507,5.10840805676518 --trim3 5 --ma 14.5469728514984 -k 2 --mp 5.2363742255102,4.7330180333492 --large-index --np 3 --cp-min 4 --cp-ival 3 --qseq -p 3 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s CGC 717s CGC 717s Processing line... 717s CGC 717s CGC 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s AG 717s AG 717s Processing line... 717s AG 717s AG 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s CGCGACGG 717s CGCGACGG 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s GCCTGCG 717s GCCTGCG 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s --- Summary --- 717s Read 1 reference strings 717s Checked 6 alignments, 0 edits 717s --------------- 717s PASSED 717s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 717s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 717s 129 reads; of these: 717s 129 (100.00%) were unpaired; of these: 717s 125 (96.90%) aligned 0 times 717s 2 (1.55%) aligned exactly 1 time 717s 2 (1.55%) aligned >1 times 717s 3.10% overall alignment rate 717s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 717s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 717s Flattened IUPAC characters 717s Mutating sequence Sim.pm.1 717s Introducing 3 SNPs, 1/1 ref/read gaps, and 0 rearrangements 717s Finished SNPs 717s Finished ref gaps 717s Finished read gaps 717s Mutating sequence Sim.pm.2 717s Introducing 5 SNPs, 0/1 ref/read gaps, and 2 rearrangements 717s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 717s Finished SNPs 717s Finished ref gaps 717s Finished read gaps 717s Mutated reference genome to subject genome 717s SNPs introduced: 8 717s Reference gaps introduced: 1 717s Read gaps introduced: 2 717s Rearrangements introduced: 2 717s Created read sampler 717s Sampling 90 reads 717s *** Run 29 of 100 717s /usr/bin/bowtie2 --cp-ival 1 --trim5 3 --large-index --cp-min 2 --rfg 5.347004623383 -k 8 --mp 2.71319422620419,2.38735749243078 --score-min L,4.2202623578358,8.407329323526 --trim3 9 --ma 30.7872967109644 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 717s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 717s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 717s parsing sequence Sim.pm.1... 717s parsing sequence Sim.pm.2... 717s Parsed 40 reference bases 717s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 717s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 717s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 717s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '5' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 717s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '6' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 717s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '7' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 717s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '9' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 717s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '11' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 717s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '14' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 717s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '16' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 717s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '22' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 717s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '26' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 717s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '27' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 717s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '28' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 717s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '35' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 717s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '43' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 717s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '44' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 717s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '45' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 717s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '46' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 717s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '51' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 717s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '52' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 717s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '54' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 717s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 717s Warning: skipping read '57' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 717s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '61' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 717s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '64' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 717s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '68' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 717s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '70' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 717s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '71' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 717s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '72' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 717s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '73' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 717s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '76' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 717s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '78' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 717s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '83' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 717s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '84' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 717s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '89' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 717s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '90' because it was < 2 characters long 717s 90 reads; of these: 717s 90 (100.00%) were unpaired; of these: 717s 81 (90.00%) aligned 0 times 717s 4 (4.44%) aligned exactly 1 time 717s 5 (5.56%) aligned >1 times 717s 10.00% overall alignment rate 717s Read 50 alignments... 717s Read 100 alignments... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s AC 717s AC 717s Processing line... 717s AC 717s AC 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s CCGGGGG 717s CCGGGGG 717s Processing line... 717s GA 717s GA 717s Processing line... 717s TC 717s TC 717s Processing line... 717s GA 717s GA 717s Processing line... 717s GA 717s GA 717s Processing line... 717s GA 717s GA 717s Processing line... 717s TC 717s TC 717s Processing line... 717s Processing line... 717s ACG 717s ACG 717s Processing line... 717s Processing line... 717s Processing line... 717s GCG 717s GCG 717s Processing line... 717s CGC 717s CGC 717s Processing line... 717s GCG 717s GCG 717s Processing line... 717s GCG 717s GCG 717s Processing line... 717s CGC 717s CGC 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s TTCGCGAGGAG 717s TTCGCGAGGAG 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s CATC 717s CATC 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s AT 717s AT 717s Processing line... 717s AT 717s AT 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s GAGGAG 717s GAGGAG 717s Processing line... 717s GAGGAG 717s GAGGAG 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s --- Summary --- 717s Read 1 reference strings 717s Checked 21 alignments, 0 edits 717s --------------- 717s PASSED 717s Flattened IUPAC characters 717s Mutating sequence Sim.pm.2 717s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 717s Finished SNPs 717s Finished ref gaps 717s Finished read gaps 717s Mutating sequence Sim.pm.1 717s Introducing 11 SNPs, 1/1 ref/read gaps, and 1 rearrangements 717s Finished SNPs 717s Finished ref gaps 717s Finished read gaps 717s Mutated reference genome to subject genome 717s SNPs introduced: 14 717s Reference gaps introduced: 2 717s Read gaps introduced: 1 717s Rearrangements introduced: 1 717s Created read sampler 717s Sampling 167 reads 717s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 717s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 717s parsing sequence Sim.pm.1... 717s parsing sequence Sim.pm.2... 717s Parsed 40 reference bases 717s *** Run 30 of 100 717s /usr/bin/bowtie2 --cp-ival 4 --n-ceil 1.20353602725107,1.08034352996815 --large-index --cp-min 7 --rdg 27.1768705388689 -D 19 --mp 5.18987272825985,5.16953951279207 -N 0 -L23 --score-min L,6.84045767664858,8.10418749454242 --ma 6.44192129912009 --nofw --trim3 7 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 717s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 717s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 717s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '2' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 717s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 717s Warning: skipping read '6' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 717s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '12' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 717s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '18' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 717s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '19' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 717s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '20' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 717s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '23' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 717s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '34' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 717s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '52' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 717s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 717s Warning: skipping read '55' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 717s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '59' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 717s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 717s Warning: skipping read '62' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 717s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 717s Warning: skipping read '63' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 717s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '64' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 717s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '68' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 717s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '72' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 717s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '75' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 717s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '78' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 717s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '84' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 717s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '87' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 717s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '97' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 717s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '101' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 717s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '112' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 717s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '114' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 717s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '125' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 717s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '126' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 717s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '127' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 717s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '136' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 717s Warning: skipping read '139' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '139' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 717s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '146' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 717s Warning: skipping read '151' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '151' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 717s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '154' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 717s Warning: skipping read '155' because length (1) <= # seed mismatches (0) 717s Warning: skipping read '155' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 717s /usr/bin/bowtie2 --cp-ival 4 --n-ceil 1.20353602725107,1.08034352996815 --large-index --cp-min 7 --rdg 27.1768705388689 -D 19 --mp 5.18987272825985,5.16953951279207 -N 0 -L23 --score-min L,6.84045767664858,8.10418749454242 --ma 6.44192129912009 --nofw --trim3 7 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 717s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 717s 167 reads; of these: 717s 167 (100.00%) were unpaired; of these: 717s 161 (96.41%) aligned 0 times 717s 4 (2.40%) aligned exactly 1 time 717s 2 (1.20%) aligned >1 times 717s 3.59% overall alignment rate 717s Read 50 alignments... 717s Read 100 alignments... 717s Read 150 alignments... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s ACATCTTCGCGAGGA 717s ACATCTTCGCGAGGA 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s TCT 717s TCT 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s CCT 717s CCT 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s ACG 717s ACG 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s CGA 717s CGA 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s GC 717s GC 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s --- Summary --- 717s Read 1 reference strings 717s Checked 6 alignments, 0 edits 717s --------------- 717s PASSED 717s ALSO checking that bowtie2 and bowtie2-align match up 717s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 717s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 717s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '2' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 717s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 717s Warning: skipping read '6' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 717s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '12' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 717s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '18' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 717s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '19' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 717s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '20' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 717s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '23' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 717s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '34' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 717s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '52' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 717s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 717s Warning: skipping read '55' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 717s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '59' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 717s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 717s Warning: skipping read '62' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 717s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 717s Warning: skipping read '63' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 717s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '64' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 717s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '68' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 717s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '72' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 717s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '75' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 717s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '78' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 717s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '84' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 717s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '87' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 717s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '97' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 717s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '101' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 717s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '112' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 717s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '114' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 717s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '125' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 717s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '126' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 717s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '127' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 717s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '136' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 717s Warning: skipping read '139' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '139' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 717s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '146' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 717s Warning: skipping read '151' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '151' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 717s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 717s Warning: skipping read '154' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 717s Warning: skipping read '155' because length (1) <= # seed mismatches (0) 717s Warning: skipping read '155' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 717s 167 reads; of these: 717s 167 (100.00%) were unpaired; of these: 717s 161 (96.41%) aligned 0 times 717s 4 (2.40%) aligned exactly 1 time 717s 2 (1.20%) aligned >1 times 717s 3.59% overall alignment rate 717s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 717s Flattened IUPAC characters 717s Mutating sequence Sim.pm.2 717s Introducing 3 SNPs, 1/1 ref/read gaps, and 0 rearrangements 717s Finished SNPs 717s Finished ref gaps 717s Finished read gaps 717s Mutating sequence Sim.pm.1 717s Introducing 12 SNPs, 0/0 ref/read gaps, and 0 rearrangements 717s Finished SNPs 717s Finished ref gaps 717s Finished read gaps 717s Mutated reference genome to subject genome 717s SNPs introduced: 15 717s Reference gaps introduced: 1 717s Read gaps introduced: 1 717s Rearrangements introduced: 0 717s Created read sampler 717s Sampling 145 reads 717s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 717s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 717s parsing sequence Sim.pm.1... 717s parsing sequence Sim.pm.2... 717s Parsed 40 reference bases 717s *** Run 31 of 100 717s /usr/bin/bowtie2 --trim5 4 --cp-ival 1 --mp 5.1847451951836,4.6952032098045 --trim3 7 --large-index --cp-min 2 -k 15 -D 24 -R 3 --score-min L,8.01550351889702,3.25089391429256 --mm --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_138_138_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_143_143_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_143_143_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 717s Read 50 alignments... 717s Read 100 alignments... 717s Read 150 alignments... 717s 145 reads; of these: 717s 145 (100.00%) were unpaired; of these: 717s 135 (93.10%) aligned 0 times 717s 5 (3.45%) aligned exactly 1 time 717s 5 (3.45%) aligned >1 times 717s 6.90% overall alignment rate 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s CGAGGAGGA 717s CGAGGAGGA 717s Processing line... 717s ACGG 717s ACGG 717s Processing line... 717s /usr/bin/bowtie2 --trim5 4 --cp-ival 1 --mp 5.1847451951836,4.6952032098045 --trim3 7 --large-index --cp-min 2 -k 15 -D 24 -R 3 --score-min L,8.01550351889702,3.25089391429256 --mm --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s GGG 717s GGG 717s Processing line... 717s GGG 717s GGG 717s Processing line... 717s GGG 717s GGG 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s GCGAC 717s GCGAC 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s GA 717s GA 717s Processing line... 717s GA 717s GA 717s Processing line... 717s TC 717s TC 717s Processing line... 717s GA 717s GA 717s Processing line... 717s GA 717s GA 717s Processing line... 717s TC 717s TC 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s GG 717s GG 717s Processing line... 717s GG 717s GG 717s Processing line... 717s CC 717s CC 717s Processing line... 717s GG 717s GG 717s Processing line... 717s CC 717s CC 717s Processing line... 717s GG 717s GG 717s Processing line... 717s GG 717s GG 717s Processing line... 717s GG 717s GG 717s Processing line... 717s GG 717s GG 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s ATC 717s ATC 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s CGAC 717s CGAC 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s AC 717s AC 717s Processing line... 717s AC 717s AC 717s Processing line... 717s Processing line... 717s GCG 717s GCG 717s Processing line... 717s GCG 717s GCG 717s Processing line... 717s CGC 717s CGC 717s Processing line... 717s GCG 717s GCG 717s Processing line... 717s CGC 717s CGC 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s --- Summary --- 717s Read 1 reference strings 717s Checked 30 alignments, 0 edits 717s --------------- 717s PASSED 717s ALSO checking that bowtie2 and bowtie2-align match up 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_138_138_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_143_143_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_143_143_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 717s 145 reads; of these: 717s 145 (100.00%) were unpaired; of these: 717s 135 (93.10%) aligned 0 times 717s 5 (3.45%) aligned exactly 1 time 717s 5 (3.45%) aligned >1 times 717s 6.90% overall alignment rate 717s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 717s Flattened IUPAC characters 717s Mutating sequence Sim.pm.2 717s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 717s Finished SNPs 717s Finished ref gaps 717s Finished read gaps 717s Mutating sequence Sim.pm.1 717s Introducing 2 SNPs, 1/3 ref/read gaps, and 0 rearrangements 717s Finished SNPs 717s Finished ref gaps 717s Finished read gaps 717s Mutated reference genome to subject genome 717s SNPs introduced: 3 717s Reference gaps introduced: 1 717s Read gaps introduced: 3 717s Rearrangements introduced: 0 717s Created read sampler 717s Sampling 29 reads 717s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 717s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 717s parsing sequence Sim.pm.1... 717s parsing sequence Sim.pm.2... 717s Parsed 40 reference bases 717s *** Run 32 of 100 717s /usr/bin/bowtie2 -R 1 -k 2 --gbar 5 --score-min L,1.73443129073207,5.25969140281611 --cp-min 5 --large-index -N 0 -L15 -i L,0.249757064846042 --mp 5.40109991938504,3.77586582440352 --nofw --cp-ival 2 --local --n-ceil 1.30438323173326,0.469827285937648 --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq 717s Warning: skipping mate #2 of read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping mate #2 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 717s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 717s 29 reads; of these: 717s 29 (100.00%) were paired; of these: 717s 29 (100.00%) aligned concordantly 0 times 717s 0 (0.00%) aligned concordantly exactly 1 time 717s 0 (0.00%) aligned concordantly >1 times 717s ---- 717s 29 pairs aligned concordantly 0 times; of these: 717s 0 (0.00%) aligned discordantly 1 time 717s ---- 717s 29 pairs aligned 0 times concordantly or discordantly; of these: 717s 58 mates make up the pairs; of these: 717s 58 (100.00%) aligned 0 times 717s 0 (0.00%) aligned exactly 1 time 717s 0 (0.00%) aligned >1 times 717s 0.00% overall alignment rate 717s Read 50 alignments... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s --- Summary --- 717s Read 1 reference strings 717s Checked 0 alignments, 0 edits 717s --------------- 717s PASSED 717s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 717s /usr/bin/bowtie2 -R 1 -k 2 --gbar 5 --score-min L,1.73443129073207,5.25969140281611 --cp-min 5 --large-index -N 0 -L15 -i L,0.249757064846042 --mp 5.40109991938504,3.77586582440352 --nofw --cp-ival 2 --local --n-ceil 1.30438323173326,0.469827285937648 --qseq -p 2 -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 717s Warning: skipping mate #2 of read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping mate #2 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 717s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 717s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 717s 29 reads; of these: 717s 29 (100.00%) were paired; of these: 717s 29 (100.00%) aligned concordantly 0 times 717s 0 (0.00%) aligned concordantly exactly 1 time 717s 0 (0.00%) aligned concordantly >1 times 717s ---- 717s 29 pairs aligned concordantly 0 times; of these: 717s 0 (0.00%) aligned discordantly 1 time 717s ---- 717s 29 pairs aligned 0 times concordantly or discordantly; of these: 717s 58 mates make up the pairs; of these: 717s 58 (100.00%) aligned 0 times 717s 0 (0.00%) aligned exactly 1 time 717s 0 (0.00%) aligned >1 times 717s 0.00% overall alignment rate 717s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 717s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 717s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 717s Flattened IUPAC characters 717s Mutating sequence Sim.pm.2 717s Introducing 13 SNPs, 0/0 ref/read gaps, and 1 rearrangements 717s Finished SNPs 717s Finished ref gaps 717s Finished read gaps 717s Mutating sequence Sim.pm.1 717s Introducing 6 SNPs, 1/0 ref/read gaps, and 1 rearrangements 717s Finished SNPs 717s Finished ref gaps 717s Finished read gaps 717s Mutated reference genome to subject genome 717s SNPs introduced: 19 717s Reference gaps introduced: 1 717s Read gaps introduced: 0 717s Rearrangements introduced: 2 717s Created read sampler 717s Sampling 70 reads 717s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 717s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 717s parsing sequence Sim.pm.1... 717s parsing sequence Sim.pm.2... 717s Parsed 40 reference bases 717s *** Run 33 of 100 717s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 0.393067158251399,1.4709282177635 --np 1 --cp-min 2 --large-index --gbar 3 --trim3 5 --score-min L,7.25710148450622,7.43899054653672 --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 717s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 717s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 717s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 717s 70 reads; of these: 717s 70 (100.00%) were unpaired; of these: 717s 65 (92.86%) aligned 0 times 717s 4 (5.71%) aligned exactly 1 time 717s 1 (1.43%) aligned >1 times 717s 7.14% overall alignment rate 717s Read 50 alignments... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s AT 717s AT 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s GAC 717s GAC 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s GCGCGACG 717s GCGCGACG 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s GGGGCCTGCGCGACG 717s GGGGCCTGCGCGACG 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s TCTTCGCGA 717s TCTTCGCGA 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s Processing line... 717s --- Summary --- 717s Read 1 reference strings 717s Checked 5 alignments, 0 edits 717s --------------- 717s PASSED 717s Flattened IUPAC characters 717s Mutating sequence Sim.pm.2 717s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 717s Finished SNPs 717s Finished ref gaps 717s Finished read gaps 717s Mutating sequence Sim.pm.1 717s Introducing 10 SNPs, 3/0 ref/read gaps, and 2 rearrangements 717s Finished SNPs 717s Finished ref gaps 717s Finished read gaps 717s Mutated reference genome to subject genome 717s SNPs introduced: 10 717s Reference gaps introduced: 3 717s Read gaps introduced: 0 717s Rearrangements introduced: 3 717s Created read sampler 717s Sampling 33 reads 717s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 717s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 717s parsing sequence Sim.pm.1... 717s parsing sequence Sim.pm.2... 717s Parsed 40 reference bases 717s *** Run 34 of 100 717s /usr/bin/bowtie2 --large-index --cp-min 2 --gbar 7 --score-min L,3.19664794053653,8.54023337639861 --norc --trim5 2 -a --cp-ival 1 --local -N 1 -L16 --trim3 5 --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq 718s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 718s 33 reads; of these: 718s 33 (100.00%) were unpaired; of these: 718s 33 (100.00%) aligned 0 times 718s 0 (0.00%) aligned exactly 1 time 718s 0 (0.00%) aligned >1 times 718s 0.00% overall alignment rate 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s --- Summary --- 718s Read 1 reference strings 718s Checked 0 alignments, 0 edits 718s --------------- 718s PASSED 718s ALSO checking that bowtie2 and bowtie2-align match up 718s /usr/bin/bowtie2 --large-index --cp-min 2 --gbar 7 --score-min L,3.19664794053653,8.54023337639861 --norc --trim5 2 -a --cp-ival 1 --local -N 1 -L16 --trim3 5 --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 718s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 718s 33 reads; of these: 718s 33 (100.00%) were unpaired; of these: 718s 33 (100.00%) aligned 0 times 718s 0 (0.00%) aligned exactly 1 time 718s 0 (0.00%) aligned >1 times 718s 0.00% overall alignment rate 718s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 718s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 718s /usr/bin/bowtie2 --large-index --cp-min 2 --gbar 7 --score-min L,3.19664794053653,8.54023337639861 --norc --trim5 2 -a --cp-ival 1 --local -N 1 -L16 --trim3 5 --qseq -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 718s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 718s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 718s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 718s 33 reads; of these: 718s 33 (100.00%) were unpaired; of these: 718s 33 (100.00%) aligned 0 times 718s 0 (0.00%) aligned exactly 1 time 718s 0 (0.00%) aligned >1 times 718s 0.00% overall alignment rate 718s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 718s Flattened IUPAC characters 718s Mutating sequence Sim.pm.2 718s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 718s Finished SNPs 718s Finished ref gaps 718s Finished read gaps 718s Mutating sequence Sim.pm.1 718s Introducing 14 SNPs, 1/0 ref/read gaps, and 0 rearrangements 718s Finished SNPs 718s Finished ref gaps 718s Finished read gaps 718s *** Run 35 of 100 718s /usr/bin/bowtie2 --cp-min 3 --large-index -R 3 -D 11 --ma 6.24854961043537 --score-min L,5.20027184999693,4.00776689250962 --mm --rdg 31.5569269933453,9.51951131511408 --trim5 8 --norc --cp-ival 1 --mp 9.22524356429731,5.12287396492636 --trim3 3 -r -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.raw -2 /tmp/Sim.pm.qtk7xXsv_2.raw 718s Mutated reference genome to subject genome 718s SNPs introduced: 17 718s Reference gaps introduced: 1 718s Read gaps introduced: 0 718s Rearrangements introduced: 0 718s Created read sampler 718s Sampling 113 reads 718s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 718s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 718s parsing sequence Sim.pm.1... 718s parsing sequence Sim.pm.2... 718s Parsed 40 reference bases 718s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 718s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '0' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 718s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 718s Warning: skipping mate #2 of read '2' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 718s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '3' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 718s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '13' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 718s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '14' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 718s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '18' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 718s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '19' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 718s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 718s Warning: skipping mate #2 of read '28' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 718s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '30' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 718s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '33' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 718s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 718s Warning: skipping mate #2 of read '36' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 718s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '38' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 718s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '39' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 718s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 718s Warning: skipping read '41' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 718s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '44' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 718s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '51' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 718s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '54' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 718s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '57' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 718s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '59' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 718s Read 50 alignments... 718s Read 100 alignments... 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 718s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '69' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 718s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '70' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 718s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '72' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 718s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '74' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 718s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '75' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 718s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 718s Warning: skipping mate #2 of read '77' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 718s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '81' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 718s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '84' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 718s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '90' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 718s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '92' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 718s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '96' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 718s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '100' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 718s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '108' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 718s 113 reads; of these: 718s 85 (75.22%) were paired; of these: 718s 85 (100.00%) aligned concordantly 0 times 718s 0 (0.00%) aligned concordantly exactly 1 time 718s 0 (0.00%) aligned concordantly >1 times 718s ---- 718s 85 pairs aligned concordantly 0 times; of these: 718s 0 (0.00%) aligned discordantly 1 time 718s ---- 718s 85 pairs aligned 0 times concordantly or discordantly; of these: 718s 170 mates make up the pairs; of these: 718s 168 (98.82%) aligned 0 times 718s 2 (1.18%) aligned exactly 1 time 718s 0 (0.00%) aligned >1 times 718s 28 (24.78%) were unpaired; of these: 718s 27 (96.43%) aligned 0 times 718s 0 (0.00%) aligned exactly 1 time 718s 1 (3.57%) aligned >1 times 718s 1.52% overall alignment rate 718s Read 150 alignments... 718s Read 200 alignments... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s /usr/bin/bowtie2 --cp-min 3 --large-index -R 3 -D 11 --ma 6.24854961043537 --score-min L,5.20027184999693,4.00776689250962 --mm --rdg 31.5569269933453,9.51951131511408 --trim5 8 --norc --cp-ival 1 --mp 9.22524356429731,5.12287396492636 --trim3 3 -r -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.raw -2 /tmp/Sim.pm.qtk7xXsv_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s CA 718s CA 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s CTTCGC 718s CTTCGC 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s CC 718s CC 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s --- Summary --- 718s Read 1 reference strings 718s Checked 3 alignments, 0 edits 718s --------------- 718s PASSED 718s ALSO checking that bowtie2 and bowtie2-align match up 718s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 718s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '0' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 718s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 718s Warning: skipping mate #2 of read '2' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 718s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '3' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 718s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '13' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 718s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '14' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 718s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '18' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 718s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '19' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 718s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 718s Warning: skipping mate #2 of read '28' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 718s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '30' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 718s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '33' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 718s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 718s Warning: skipping mate #2 of read '36' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 718s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '38' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 718s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '39' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 718s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 718s Warning: skipping read '41' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 718s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '44' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 718s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '51' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 718s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '54' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 718s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '57' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 718s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '59' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 718s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '69' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 718s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '70' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 718s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '72' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 718s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '74' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 718s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '75' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 718s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 718s Warning: skipping mate #2 of read '77' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 718s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '81' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 718s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '84' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 718s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '90' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 718s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '92' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 718s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '96' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 718s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 718s Warning: skipping mate #1 of read '100' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 718s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '108' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 718s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 718s *** Run 36 of 100 718s /usr/bin/bowtie2 --cp-ival 1 -a --trim5 9 --rfg 42.3202727559131 --trim3 7 -i C,1.48822840373005 --mp 9.96765203832203,8.83281473619363 --large-index --cp-min 8 --rdg 47.8175718050886,19.4120613401873 --score-min L,8.16119579584414,4.84084558508912 --ma 8.7993229184963 -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta 718s 113 reads; of these: 718s 85 (75.22%) were paired; of these: 718s 85 (100.00%) aligned concordantly 0 times 718s 0 (0.00%) aligned concordantly exactly 1 time 718s 0 (0.00%) aligned concordantly >1 times 718s ---- 718s 85 pairs aligned concordantly 0 times; of these: 718s 0 (0.00%) aligned discordantly 1 time 718s ---- 718s 85 pairs aligned 0 times concordantly or discordantly; of these: 718s 170 mates make up the pairs; of these: 718s 168 (98.82%) aligned 0 times 718s 2 (1.18%) aligned exactly 1 time 718s 0 (0.00%) aligned >1 times 718s 28 (24.78%) were unpaired; of these: 718s 27 (96.43%) aligned 0 times 718s 0 (0.00%) aligned exactly 1 time 718s 1 (3.57%) aligned >1 times 718s 1.52% overall alignment rate 718s Flattened IUPAC characters 718s Mutating sequence Sim.pm.2 718s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 718s Finished SNPs 718s Finished ref gaps 718s Finished read gaps 718s Mutating sequence Sim.pm.1 718s Introducing 3 SNPs, 1/0 ref/read gaps, and 2 rearrangements 718s Finished SNPs 718s Finished ref gaps 718s Finished read gaps 718s Mutated reference genome to subject genome 718s SNPs introduced: 9 718s Reference gaps introduced: 1 718s Read gaps introduced: 0 718s Rearrangements introduced: 2 718s Created read sampler 718s Sampling 77 reads 718s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 718s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 718s parsing sequence Sim.pm.1... 718s parsing sequence Sim.pm.2... 718s Parsed 40 reference bases 718s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 718s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 718s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '1' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 718s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '5' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 718s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '7' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 718s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '9' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 718s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '10' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 718s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '11' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 718s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '12' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 718s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '13' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 718s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '14' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 718s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '16' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 718s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '17' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 718s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '18' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 718s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 718s Warning: skipping read '19' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 718s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '20' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 718s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '22' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 718s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '23' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 718s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '25' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 718s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '27' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 718s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '30' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 718s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '33' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 718s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '34' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 718s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '35' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 718s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '38' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 718s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '41' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 718s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '42' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 718s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '43' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 718s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '44' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 718s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '45' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 718s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '46' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 718s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '48' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 718s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '50' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 718s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '51' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 718s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '52' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 718s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '53' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 718s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '59' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 718s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '63' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 718s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '64' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 718s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '65' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 718s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '67' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 718s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '71' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 718s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 718s Warning: skipping read '74' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 718s 77 reads; of these: 718s 77 (100.00%) were unpaired; of these: 718s 75 (97.40%) aligned 0 times 718s 1 (1.30%) aligned exactly 1 time 718s 1 (1.30%) aligned >1 times 718s 2.60% overall alignment rate 718s Read 50 alignments... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s CC 718s CC 718s Processing line... 718s GG 718s GG 718s Processing line... 718s GG 718s GG 718s Processing line... 718s CC 718s CC 718s Processing line... 718s GG 718s GG 718s Processing line... 718s *** Run 37 of 100 718s /usr/bin/bowtie2 --large-index --np 1 --cp-min 2 --cp-ival 4 --score-min L,9.74210156131472,1.76343501959554 --ma 36.6777205893799 --gbar 1 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 718s GG 718s GG 718s Processing line... 718s GG 718s GG 718s Processing line... 718s GG 718s GG 718s Processing line... 718s GG 718s GG 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s CATCTTCGCGAGGAG 718s CATCTTCGCGAGGAG 718s Processing line... 718s Processing line... 718s --- Summary --- 718s Read 1 reference strings 718s Checked 10 alignments, 0 edits 718s --------------- 718s PASSED 718s Flattened IUPAC characters 718s Mutating sequence Sim.pm.2 718s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 718s Finished SNPs 718s Finished ref gaps 718s Finished read gaps 718s Mutating sequence Sim.pm.1 718s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 718s Finished SNPs 718s Finished ref gaps 718s Finished read gaps 718s Mutated reference genome to subject genome 718s SNPs introduced: 6 718s Reference gaps introduced: 0 718s Read gaps introduced: 1 718s Rearrangements introduced: 1 718s Created read sampler 718s Sampling 115 reads 718s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 718s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 718s parsing sequence Sim.pm.1... 718s parsing sequence Sim.pm.2... 718s Parsed 40 reference bases 718s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 718s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 718s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 718s Warning: skipping read '2' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 718s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 718s Warning: skipping read '54' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 718s Warning: skipping read '112' because length (1) <= # seed mismatches (0) 718s Warning: skipping read '112' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 718s 115 reads; of these: 718s 115 (100.00%) were unpaired; of these: 718s 102 (88.70%) aligned 0 times 718s 11 (9.57%) aligned exactly 1 time 718s 2 (1.74%) aligned >1 times 718s 11.30% overall alignment rate 718s Read 50 alignments... 718s Read 100 alignments... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s CGACGG 718s CGACGG 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s GGGGGC 718s GGGGGC 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s GC 718s GC 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s CGCGACGG 718s CGCGACGG 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s TTCGCGAG 718s TTCGCGAG 718s Processing line... 718s Processing line... 718s Processing line... 718s CGGGG 718s CGGGG 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s TT 718s TT 718s Processing line... 718s Processing line... 718s CGCGA 718s CGCGA 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s TT 718s TT 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s GCGAG 718s GCGAG 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s CGGGGG 718s CGGGGG 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s CTTCGC 718s CTTCGC 718s Processing line... 718s Processing line... 718s GCGCGACG 718s GCGCGACG 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s Processing line... 718s --- Summary --- 718s Read 1 reference strings 718s Checked 13 alignments, 0 edits 718s --------------- 718s PASSED 718s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 718s /usr/bin/bowtie2 --large-index --np 1 --cp-min 2 --cp-ival 4 --score-min L,9.74210156131472,1.76343501959554 --ma 36.6777205893799 --gbar 1 -q -p 3 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 718s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 718s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 718s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 718s Warning: skipping read '2' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 718s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 718s Warning: skipping read '54' because it was < 2 characters long 718s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 718s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 718s Warning: skipping read '112' because length (1) <= # seed mismatches (0) 718s Warning: skipping read '112' because it was < 2 characters long 718s 115 reads; of these: 718s 115 (100.00%) were unpaired; of these: 718s 102 (88.70%) aligned 0 times 718s 11 (9.57%) aligned exactly 1 time 718s 2 (1.74%) aligned >1 times 718s 11.30% overall alignment rate 718s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 718s Flattened IUPAC characters 718s Mutating sequence Sim.pm.1 718s Introducing 13 SNPs, 0/1 ref/read gaps, and 0 rearrangements 718s Finished SNPs 718s Finished ref gaps 718s Finished read gaps 718s Mutating sequence Sim.pm.2 718s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 718s Finished SNPs 718s Finished ref gaps 718s Finished read gaps 718s Mutated reference genome to subject genome 718s SNPs introduced: 13 718s Reference gaps introduced: 0 718s Read gaps introduced: 1 718s Rearrangements introduced: 0 718s Created read sampler 718s Sampling 76 reads 718s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 718s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 718s parsing sequence Sim.pm.1... 718s parsing sequence Sim.pm.2... 718s Parsed 40 reference bases 718s *** Run 38 of 100 718s /usr/bin/bowtie2 --np 7 --cp-min 5 --large-index --ma 23.9306354518533 --score-min L,7.76497438690757,1.12470215074703 --cp-ival 1 --n-ceil 0.432658067334413,0.371033607301236 --rfg 7.41913243784861 --mp 8.03539027646565,1.83783727940925 --trim3 9 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 719s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 719s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 719s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '0' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 719s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '3' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 719s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '9' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 719s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '10' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 719s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '14' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 719s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '18' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 719s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '20' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 719s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '23' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 719s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '26' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 719s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '29' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 719s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '33' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 719s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '43' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 719s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '44' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 719s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '49' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 719s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '52' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 719s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '53' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 719s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 719s Warning: skipping read '55' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 719s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '56' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 719s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '65' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 719s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '68' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 719s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '70' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 719s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '71' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 719s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 719s Warning: skipping read '72' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 719s 76 reads; of these: 719s 76 (100.00%) were unpaired; of these: 719s 74 (97.37%) aligned 0 times 719s 1 (1.32%) aligned exactly 1 time*** Run 39 of 100 719s /usr/bin/bowtie2 -D 13 --ma 33.2913700536669 --score-min L,4.72955269460193,2.81508887805164 --cp-min 3 --np 1 --large-index -N 1 -L29 --trim3 7 --rfg 35.0214991158934,10.2863660586724 --n-ceil 0.854337002671624,1.2769911934362 --trim5 0 --norc --cp-ival 3 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 719s 719s 1 (1.32%) aligned >1 times 719s 2.63% overall alignment rate 719s Read 50 alignments... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s CG 719s CG 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s CTGCGC 719s CTGCGC 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s --- Summary --- 719s Read 1 reference strings 719s Checked 2 alignments, 0 edits 719s --------------- 719s PASSED 719s Flattened IUPAC characters 719s Mutating sequence Sim.pm.2 719s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 719s Finished SNPs 719s Finished ref gaps 719s Finished read gaps 719s Mutating sequence Sim.pm.1 719s Introducing 18 SNPs, 1/2 ref/read gaps, and 1 rearrangements 719s Finished SNPs 719s Finished ref gaps 719s Finished read gaps 719s Mutated reference genome to subject genome 719s SNPs introduced: 24 719s Reference gaps introduced: 1 719s Read gaps introduced: 2 719s Rearrangements introduced: 1 719s Created read sampler 719s Sampling 172 reads 719s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 719s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 719s parsing sequence Sim.pm.1... 719s parsing sequence Sim.pm.2... 719s Parsed 40 reference bases 719s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 719s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 719s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '3' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 719s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '4' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 719s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '5' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 719s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '12' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 719s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '13' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 719s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '15' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 719s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '18' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 719s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '26' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 719s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '28' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 719s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '33' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 719s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '39' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 719s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '43' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 719s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '45' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 719s Warning: skipping read '48' because length (1) <= # seed mismatches (1) 719s Warning: skipping read '48' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 719s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '51' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 719s Warning: skipping read '64' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '64' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 719s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '70' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 719s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '75' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 719s Warning: skipping read '78' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '78' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 719s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '81' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 719s Warning: skipping read '85' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '85' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 719s Warning: skipping read '87' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '87' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 719s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '88' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 719s Warning: skipping read '93' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '93' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 719s Warning: skipping read '106' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '106' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 719s Warning: skipping read '113' because length (1) <= # seed mismatches (1) 719s Warning: skipping read '113' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 719s Warning: skipping read '124' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '124' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 719s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '125' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 719s Warning: skipping read '126' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '126' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 719s Warning: skipping read '127' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '127' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 719s Warning: skipping read '128' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '128' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 719s Warning: skipping read '132' because length (1) <= # seed mismatches (1) 719s Warning: skipping read '132' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 719s Warning: skipping read '141' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '141' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 719s Warning: skipping read '142' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '142' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 719s Warning: skipping read '148' because length (1) <= # seed mismatches (1) 719s Warning: skipping read '148' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 719s Warning: skipping read '153' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '153' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 719s Warning: skipping read '158' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '158' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 719s Warning: skipping read '162' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '162' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 719s Warning: skipping read '165' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '165' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 719s Warning: skipping read '166' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '166' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 719s Warning: skipping read '170' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '170' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 719s Read 50 alignments... 719s 172 reads; of these: 719s 172 (100.00%) were unpaired; of these: 719s 165 (95.93%) aligned 0 times 719s 2 (1.16%) aligned exactly 1 time 719s 5 (2.91%) aligned >1 times 719s 4.07% overall alignment rate 719s Read 100 alignments... 719s Read 150 alignments... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s GGA 719s GGA 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s TG 719s TG 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s GCG 719s GCG 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s CG 719s CG 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s GGC 719s GGC 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s CA 719s CA 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s CGA 719s CGA 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s --- Summary --- 719s Read 1 reference strings 719s Checked 7 alignments, 0 edits 719s --------------- 719s PASSED 719s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 719s /usr/bin/bowtie2 -D 13 --ma 33.2913700536669 --score-min L,4.72955269460193,2.81508887805164 --cp-min 3 --np 1 --large-index -N 1 -L29 --trim3 7 --rfg 35.0214991158934,10.2863660586724 --n-ceil 0.854337002671624,1.2769911934362 --trim5 0 --norc --cp-ival 3 -q -p 4 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 719s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 719s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 719s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '3' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 719s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '4' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 719s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '5' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 719s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '12' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 719s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '13' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 719s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '15' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 719s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '18' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 719s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '26' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 719s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '28' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 719s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '33' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 719s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '39' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 719s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '43' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 719s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '45' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 719s Warning: skipping read '48' because length (1) <= # seed mismatches (1) 719s Warning: skipping read '48' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 719s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '51' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 719s Warning: skipping read '64' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '64' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 719s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '70' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 719s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '75' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 719s Warning: skipping read '78' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '78' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 719s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '81' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 719s Warning: skipping read '85' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '85' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 719s Warning: skipping read '87' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '87' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 719s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '88' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 719s Warning: skipping read '93' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '93' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 719s Warning: skipping read '106' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '106' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 719s Warning: skipping read '113' because length (1) <= # seed mismatches (1) 719s Warning: skipping read '113' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 719s Warning: skipping read '124' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '124' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 719s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '125' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 719s Warning: skipping read '126' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '126' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 719s Warning: skipping read '127' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '127' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 719s Warning: skipping read '128' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '128' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 719s Warning: skipping read '132' because length (1) <= # seed mismatches (1) 719s Warning: skipping read '132' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 719s Warning: skipping read '141' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '141' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 719s Warning: skipping read '142' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '142' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 719s Warning: skipping read '148' because length (1) <= # seed mismatches (1) 719s Warning: skipping read '148' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 719s Warning: skipping read '153' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '153' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 719s Warning: skipping read '158' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '158' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 719s Warning: skipping read '162' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '162' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 719s Warning: skipping read '165' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '165' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 719s Warning: skipping read '166' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '166' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 719s Warning: skipping read '170' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '170' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 719s 172 reads; of these: 719s 172 (100.00%) were unpaired; of these: 719s 165 (95.93%) aligned 0 times 719s 2 (1.16%) aligned exactly 1 time 719s 5 (2.91%) aligned >1 times 719s 4.07% overall alignment rate 719s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 719s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 719s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 719s /usr/bin/bowtie2 -D 13 --ma 33.2913700536669 --score-min L,4.72955269460193,2.81508887805164 --cp-min 3 --np 1 --large-index -N 1 -L29 --trim3 7 --rfg 35.0214991158934,10.2863660586724 --n-ceil 0.854337002671624,1.2769911934362 --trim5 0 --norc --cp-ival 3 -q -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 719s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 719s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 719s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 719s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '3' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 719s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '4' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 719s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '5' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 719s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '12' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 719s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '13' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 719s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '15' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 719s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '18' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 719s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '26' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 719s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '28' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 719s Warning: skipping read '33' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '33' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 719s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '39' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 719s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '43' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 719s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '45' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 719s Warning: skipping read '48' because length (1) <= # seed mismatches (1) 719s Warning: skipping read '48' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 719s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '51' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 719s Warning: skipping read '64' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '64' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 719s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '81' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 719s Warning: skipping read '85' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '85' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 719s Warning: skipping read '87' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '87' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 719s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '88' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 719s Warning: skipping read '93' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '93' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 719s Warning: skipping read '106' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '106' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 719s Warning: skipping read '113' because length (1) <= # seed mismatches (1) 719s Warning: skipping read '113' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 719s Warning: skipping read '124' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '124' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 719s Warning: skipping read '125' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '125' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 719s Warning: skipping read '126' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '126' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 719s Warning: skipping read '127' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '127' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 719s Warning: skipping read '128' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '128' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 719s Warning: skipping read '132' because length (1) <= # seed mismatches (1) 719s Warning: skipping read '132' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 719s Warning: skipping read '141' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '141' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 719s Warning: skipping read '142' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '142' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 719s Warning: skipping read '148' because length (1) <= # seed mismatches (1) 719s Warning: skipping read '148' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 719s Warning: skipping read '153' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '153' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 719s Warning: skipping read '158' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '158' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 719s Warning: skipping read '162' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '162' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 719s Warning: skipping read '165' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '165' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 719s Warning: skipping read '166' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '166' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 719s Warning: skipping read '170' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '170' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 719s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '70' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 719s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '75' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 719s Warning: skipping read '78' because length (0) <= # seed mismatches (1) 719s Warning: skipping read '78' because it was < 2 characters long 719s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 719s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 719s 172 reads; of these: 719s 172 (100.00%) were unpaired; of these: 719s 165 (95.93%) aligned 0 times 719s 2 (1.16%) aligned exactly 1 time 719s 5 (2.91%) aligned >1 times 719s 4.07% overall alignment rate 719s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 719s Flattened IUPAC characters 719s Mutating sequence Sim.pm.2 719s Introducing 7 SNPs, 0/2 ref/read gaps, and 1 rearrangements 719s Finished SNPs 719s Finished ref gaps 719s Finished read gaps 719s Mutating sequence Sim.pm.1 719s Introducing 13 SNPs, 0/0 ref/read gaps, and 0 rearrangements 719s Finished SNPs 719s Finished ref gaps 719s Finished read gaps 719s Mutated reference genome to subject genome 719s SNPs introduced: 20 719s Reference gaps introduced: 0 719s Read gaps introduced: 2 719s Rearrangements introduced: 1 719s Created read sampler 719s Sampling 41 reads 719s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 719s *** Run 40 of 100 719s /usr/bin/bowtie2 --cp-ival 1 --local --large-index --cp-min 13 --np 12 --rfg 23.4105703983915 --rdg 45.5534607721698 -k 2 --mp 7.71296867802848,1.65090317899677 --score-min L,4.19655804974373,6.16174973722022 -r -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.raw -2 /tmp/Sim.pm.qtk7xXsv_2.raw 719s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 719s parsing sequence Sim.pm.1... 719s parsing sequence Sim.pm.2... 719s Parsed 40 reference bases 719s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 719s Warning: skipping mate #2 of read '4' because it was < 2 characters long 719s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (0) 719s Warning: skipping mate #2 of read '20' because it was < 2 characters long 719s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 719s Warning: skipping mate #1 of read '38' because it was < 2 characters long 719s 41 reads; of these: 719s 41 (100.00%) were paired; of these: 719s 41 (100.00%) aligned concordantly 0 times 719s 0 (0.00%) aligned concordantly exactly 1 time 719s 0 (0.00%) aligned concordantly >1 times 719s ---- 719s 41 pairs aligned concordantly 0 times; of these: 719s 0 (0.00%) aligned discordantly 1 time 719s ---- 719s 41 pairs aligned 0 times concordantly or discordantly; of these: 719s 82 mates make up the pairs; of these: 719s 82 (100.00%) aligned 0 times 719s 0 (0.00%) aligned exactly 1 time 719s 0 (0.00%) aligned >1 times 719s 0.00% overall alignment rate 719s Read 50 alignments... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s /usr/bin/bowtie2 --cp-ival 1 --local --large-index --cp-min 13 --np 12 --rfg 23.4105703983915 --rdg 45.5534607721698 -k 2 --mp 7.71296867802848,1.65090317899677 --score-min L,4.19655804974373,6.16174973722022 -r -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.raw -2 /tmp/Sim.pm.qtk7xXsv_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s Processing line... 719s --- Summary --- 719s Read 1 reference strings 719s Checked 0 alignments, 0 edits 719s --------------- 719s PASSED 719s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 720s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 720s Warning: skipping mate #2 of read '4' because it was < 2 characters long 720s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (0) 720s Warning: skipping mate #2 of read '20' because it was < 2 characters long 720s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 720s Warning: skipping mate #1 of read '38' because it was < 2 characters long 720s 41 reads; of these: 720s 41 (100.00%) were paired; of these: 720s 41 (100.00%) aligned concordantly 0 times 720s 0 (0.00%) aligned concordantly exactly 1 time 720s 0 (0.00%) aligned concordantly >1 times 720s ---- 720s 41 pairs aligned concordantly 0 times; of these: 720s 0 (0.00%) aligned discordantly 1 time 720s ---- 720s 41 pairs aligned 0 times concordantly or discordantly; of these: 720s 82 mates make up the pairs; of these: 720s 82 (100.00%) aligned 0 times 720s 0 (0.00%) aligned exactly 1 time 720s 0 (0.00%) aligned >1 times 720s 0.00% overall alignment rate 720s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 720s Flattened IUPAC characters 720s Mutating sequence Sim.pm.1 720s Introducing 16 SNPs, 0/0 ref/read gaps, and 0 rearrangements 720s Finished SNPs 720s Finished ref gaps 720s Finished read gaps 720s Mutating sequence Sim.pm.2 720s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 720s Finished SNPs 720s Finished ref gaps 720s Finished read gaps 720s Mutated reference genome to subject genome 720s SNPs introduced: 23 720s Reference gaps introduced: 0 720s Read gaps introduced: 1 720s Rearrangements introduced: 0 720s Created read sampler 720s Sampling 85 reads 720s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 720s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 720s parsing sequence Sim.pm.1... 720s parsing sequence Sim.pm.2... 720s Parsed 40 reference bases 720s *** Run 41 of 100 720s /usr/bin/bowtie2 --mm --rdg 27.3191051767785,11.2687091710234 -D 7 -R 2 --score-min L,1.46879351783891,5.15749854798772 --large-index --cp-min 3 --trim3 7 --cp-ival 1 --local -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 720s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '0' because it was < 2 characters long 720s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '1' because it was < 2 characters long 720s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '3' because it was < 2 characters long 720s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '5' because it was < 2 characters long 720s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '10' because it was < 2 characters long 720s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '11' because it was < 2 characters long 720s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '14' because it was < 2 characters long 720s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '16' because it was < 2 characters long 720s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 720s Warning: skipping read '17' because it was < 2 characters long 720s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 720s Warning: skipping read '19' because it was < 2 characters long 720s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '20' because it was < 2 characters long 720s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 720s Warning: skipping read '21' because it was < 2 characters long 720s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '22' because it was < 2 characters long 720s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '28' because it was < 2 characters long 720s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '32' because it was < 2 characters long 720s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '34' because it was < 2 characters long 720s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '35' because it was < 2 characters long 720s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '37' because it was < 2 characters long 720s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '48' because it was < 2 characters long 720s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '51' because it was < 2 characters long 720s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '55' because it was < 2 characters long 720s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '58' because it was < 2 characters long 720s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '66' because it was < 2 characters long 720s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '71' because it was < 2 characters long 720s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '84' because it was < 2 characters long 720s 85 reads; of these: 720s 85 (100.00%) were unpaired; of these: 720s 85 (100.00%) aligned 0 times 720s 0 (0.00%) aligned exactly 1 time 720s 0 (0.00%) aligned >1 times 720s 0.00% overall alignment rate 720s Read 50 alignments... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s /usr/bin/bowtie2 --mm --rdg 27.3191051767785,11.2687091710234 -D 7 -R 2 --score-min L,1.46879351783891,5.15749854798772 --large-index --cp-min 3 --trim3 7 --cp-ival 1 --local -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s --- Summary --- 720s Read 1 reference strings 720s Checked 0 alignments, 0 edits 720s --------------- 720s PASSED 720s ALSO checking that bowtie2 and bowtie2-align match up 720s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '0' because it was < 2 characters long 720s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '1' because it was < 2 characters long 720s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '3' because it was < 2 characters long 720s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '5' because it was < 2 characters long 720s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '10' because it was < 2 characters long 720s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '11' because it was < 2 characters long 720s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '14' because it was < 2 characters long 720s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '16' because it was < 2 characters long 720s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 720s Warning: skipping read '17' because it was < 2 characters long 720s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 720s Warning: skipping read '19' because it was < 2 characters long 720s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '20' because it was < 2 characters long 720s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 720s Warning: skipping read '21' because it was < 2 characters long 720s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '22' because it was < 2 characters long 720s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '28' because it was < 2 characters long 720s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '32' because it was < 2 characters long 720s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '34' because it was < 2 characters long 720s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '35' because it was < 2 characters long 720s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '37' because it was < 2 characters long 720s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '48' because it was < 2 characters long 720s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '51' because it was < 2 characters long 720s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '55' because it was < 2 characters long 720s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '58' because it was < 2 characters long 720s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '66' because it was < 2 characters long 720s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '71' because it was < 2 characters long 720s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 720s Warning: skipping read '84' because it was < 2 characters long 720s 85 reads; of these: 720s 85 (100.00%) were unpaired; of these: 720s 85 (100.00%) aligned 0 times 720s 0 (0.00%) aligned exactly 1 time 720s 0 (0.00%) aligned >1 times 720s 0.00% overall alignment rate 720s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 720s Flattened IUPAC characters 720s Mutating sequence Sim.pm.1 720s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 720s Finished SNPs 720s Finished ref gaps 720s Finished read gaps 720s Mutating sequence Sim.pm.2 720s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 720s *** Run 42 of 100 720s /usr/bin/bowtie2 --rfg 47.5769378654844,9.74085824935369 --score-min L,7.23268579169097,3.91494319111582 --nofw --mp 8.00594818243086,3.36474434565905 --cp-ival 2 --large-index --np 2 --cp-min 9 --n-ceil 0.599600999600294,0.165264162024229 --norc --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq 720s Finished SNPs 720s Finished ref gaps 720s Finished read gaps 720s Mutated reference genome to subject genome 720s SNPs introduced: 7 720s Reference gaps introduced: 0 720s Read gaps introduced: 1 720s Rearrangements introduced: 1 720s Created read sampler 720s Sampling 150 reads 720s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 720s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 720s parsing sequence Sim.pm.1... 720s parsing sequence Sim.pm.2... 720s Parsed 40 reference bases 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_148_148_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 720s Read 50 alignments... 720s 150 reads; of these: 720s 150 (100.00%) were unpaired; of these: 720s 150 (100.00%) aligned 0 times 720s 0 (0.00%) aligned exactly 1 time 720s 0 (0.00%) aligned >1 times 720s 0.00% overall alignment rate 720s Read 100 alignments... 720s Read 150 alignments... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s /usr/bin/bowtie2 --rfg 47.5769378654844,9.74085824935369 --score-min L,7.23268579169097,3.91494319111582 --nofw --mp 8.00594818243086,3.36474434565905 --cp-ival 2 --large-index --np 2 --cp-min 9 --n-ceil 0.599600999600294,0.165264162024229 --norc --qseq -p 3 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s Processing line... 720s --- Summary --- 720s Read 1 reference strings 720s Checked 0 alignments, 0 edits 720s --------------- 720s PASSED 720s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_148_148_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 720s 150 reads; of these: 720s 150 (100.00%) were unpaired; of these: 720s 150 (100.00%) aligned 0 times 720s 0 (0.00%) aligned exactly 1 time 720s 0 (0.00%) aligned >1 times 720s 0.00% overall alignment rate 720s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 720s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 720s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 720s /usr/bin/bowtie2 --rfg 47.5769378654844,9.74085824935369 --score-min L,7.23268579169097,3.91494319111582 --nofw --mp 8.00594818243086,3.36474434565905 --cp-ival 2 --large-index --np 2 --cp-min 9 --n-ceil 0.599600999600294,0.165264162024229 --norc --qseq -p 3 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 720s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_148_148_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 720s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 720s 150 reads; of these: 720s 150 (100.00%) were unpaired; of these: 720s 150 (100.00%) aligned 0 times 720s 0 (0.00%) aligned exactly 1 time 720s 0 (0.00%) aligned >1 times 720s 0.00% overall alignment rate 720s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 720s Flattened IUPAC characters 720s Mutating sequence Sim.pm.1 720s Introducing 6 SNPs, 3/0 ref/read gaps, and 0 rearrangements 720s Finished SNPs 720s Finished ref gaps 720s Finished read gaps 720s Mutating sequence Sim.pm.2 720s Introducing 0 SNPs, 0/2 ref/read gaps, and 0 rearrangements 720s Finished SNPs 720s Finished ref gaps 720s Finished read gaps 720s Mutated reference genome to subject genome 720s SNPs introduced: 6 720s Reference gaps introduced: 3 720s Read gaps introduced: 2 720s Rearrangements introduced: 0 720s Created read sampler 720s Sampling 120 reads 720s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 720s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 720s parsing sequence Sim.pm.1... 720s parsing sequence Sim.pm.2... 720s *** Run 43 of 100 720s /usr/bin/bowtie2 --cp-min 4 --large-index --trim5 8 --local --cp-ival 1 --score-min L,7.38593090130208,8.58018628941655 -k 2 -D 10 --rdg 9.20226201843111 --rfg 48.3503149947043,11.5073528290377 -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 720s Parsed 40 reference bases 721s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '2' because it was < 2 characters long 721s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '5' because it was < 2 characters long 721s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '10' because it was < 2 characters long 721s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '15' because it was < 2 characters long 721s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '22' because it was < 2 characters long 721s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '25' because it was < 2 characters long 721s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read '26' because it was < 2 characters long 721s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '30' because it was < 2 characters long 721s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '33' because it was < 2 characters long 721s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '39' because it was < 2 characters long 721s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '40' because it was < 2 characters long 721s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '45' because it was < 2 characters long 721s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '47' because it was < 2 characters long 721s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '53' because it was < 2 characters long 721s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '59' because it was < 2 characters long 721s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '60' because it was < 2 characters long 721s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '61' because it was < 2 characters long 721s Read 50 alignments... 721s Read 100 alignments... 721s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '69' because it was < 2 characters long 721s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '75' because it was < 2 characters long 721s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '76' because it was < 2 characters long 721s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '77' because it was < 2 characters long 721s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '81' because it was < 2 characters long 721s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '85' because it was < 2 characters long 721s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '87' because it was < 2 characters long 721s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '88' because it was < 2 characters long 721s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read '91' because it was < 2 characters long 721s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read '94' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '94' because it was < 2 characters long 721s Warning: skipping mate #2 of read '94' because it was < 2 characters long 721s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '96' because it was < 2 characters long 721s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '98' because it was < 2 characters long 721s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '101' because it was < 2 characters long 721s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '104' because it was < 2 characters long 721s Warning: skipping mate #1 of read '108' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '108' because it was < 2 characters long 721s Warning: skipping mate #2 of read '112' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read '112' because it was < 2 characters long 721s Warning: skipping mate #1 of read '114' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '114' because it was < 2 characters long 721s 120 reads; of these: 721s 105 (87.50%) were paired; of these: 721s 105 (100.00%) aligned concordantly 0 times 721s 0 (0.00%) aligned concordantly exactly 1 time 721s 0 (0.00%) aligned concordantly >1 times 721s ---- 721s 105 pairs aligned concordantly 0 times; of these: 721s 0 (0.00%) aligned discordantly 1 time 721s ---- 721s 105 pairs aligned 0 times concordantly or discordantly; of these: 721s 210 mates make up the pairs; of these: 721s 210 (100.00%) aligned 0 times 721s 0 (0.00%) aligned exactly 1 time 721s 0 (0.00%) aligned >1 times 721s 15 (12.50%) were unpaired; of these: 721s 15 (100.00%) aligned 0 times 721s 0 (0.00%) aligned exactly 1 time 721s 0 (0.00%) aligned >1 times 721s 0.00% overall alignment rate 721s Read 150 alignments... 721s Read 200 alignments... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s --- Summary --- 721s Read 1 reference strings 721s Checked 0 alignments, 0 edits 721s --------------- 721s PASSED 721s ALSO checking that bowtie2 and bowtie2-align match up 721s /usr/bin/bowtie2 --cp-min 4 --large-index --trim5 8 --local --cp-ival 1 --score-min L,7.38593090130208,8.58018628941655 -k 2 -D 10 --rdg 9.20226201843111 --rfg 48.3503149947043,11.5073528290377 -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 721s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '2' because it was < 2 characters long 721s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '5' because it was < 2 characters long 721s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '10' because it was < 2 characters long 721s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '15' because it was < 2 characters long 721s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '22' because it was < 2 characters long 721s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '25' because it was < 2 characters long 721s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read '26' because it was < 2 characters long 721s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '30' because it was < 2 characters long 721s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '33' because it was < 2 characters long 721s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '39' because it was < 2 characters long 721s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '40' because it was < 2 characters long 721s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '45' because it was < 2 characters long 721s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '47' because it was < 2 characters long 721s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '53' because it was < 2 characters long 721s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '59' because it was < 2 characters long 721s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '60' because it was < 2 characters long 721s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '61' because it was < 2 characters long 721s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '69' because it was < 2 characters long 721s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '75' because it was < 2 characters long 721s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '76' because it was < 2 characters long 721s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '77' because it was < 2 characters long 721s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '81' because it was < 2 characters long 721s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '85' because it was < 2 characters long 721s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '87' because it was < 2 characters long 721s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '88' because it was < 2 characters long 721s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read '91' because it was < 2 characters long 721s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read '94' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '94' because it was < 2 characters long 721s Warning: skipping mate #2 of read '94' because it was < 2 characters long 721s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '96' because it was < 2 characters long 721s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '98' because it was < 2 characters long 721s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '101' because it was < 2 characters long 721s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '104' because it was < 2 characters long 721s Warning: skipping mate #1 of read '108' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '108' because it was < 2 characters long 721s Warning: skipping mate #2 of read '112' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read '112' because it was < 2 characters long 721s Warning: skipping mate #1 of read '114' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '114' because it was < 2 characters long 721s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 721s 120 reads; of these: 721s 105 (87.50%) were paired; of these: 721s 105 (100.00%) aligned concordantly 0 times 721s 0 (0.00%) aligned concordantly exactly 1 time 721s 0 (0.00%) aligned concordantly >1 times 721s ---- 721s 105 pairs aligned concordantly 0 times; of these: 721s 0 (0.00%) aligned discordantly 1 time 721s ---- 721s 105 pairs aligned 0 times concordantly or discordantly; of these: 721s 210 mates make up the pairs; of these: 721s 210 (100.00%) aligned 0 times 721s 0 (0.00%) aligned exactly 1 time 721s 0 (0.00%) aligned >1 times 721s 15 (12.50%) were unpaired; of these: 721s 15 (100.00%) aligned 0 times 721s 0 (0.00%) aligned exactly 1 time 721s 0 (0.00%) aligned >1 times 721s 0.00% overall alignment rate 721s /usr/bin/bowtie2 --cp-min 4 --large-index --trim5 8 --local --cp-ival 1 --score-min L,7.38593090130208,8.58018628941655 -k 2 -D 10 --rdg 9.20226201843111 --rfg 48.3503149947043,11.5073528290377 -f -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 721s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 721s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '2' because it was < 2 characters long 721s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '5' because it was < 2 characters long 721s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '10' because it was < 2 characters long 721s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '15' because it was < 2 characters long 721s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '22' because it was < 2 characters long 721s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '25' because it was < 2 characters long 721s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read '26' because it was < 2 characters long 721s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '30' because it was < 2 characters long 721s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '33' because it was < 2 characters long 721s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '39' because it was < 2 characters long 721s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '40' because it was < 2 characters long 721s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '45' because it was < 2 characters long 721s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '47' because it was < 2 characters long 721s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '53' because it was < 2 characters long 721s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '59' because it was < 2 characters long 721s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '60' because it was < 2 characters long 721s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '61' because it was < 2 characters long 721s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '69' because it was < 2 characters long 721s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '75' because it was < 2 characters long 721s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '76' because it was < 2 characters long 721s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '77' because it was < 2 characters long 721s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '81' because it was < 2 characters long 721s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '85' because it was < 2 characters long 721s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '87' because it was < 2 characters long 721s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '88' because it was < 2 characters long 721s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read '91' because it was < 2 characters long 721s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read '94' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '94' because it was < 2 characters long 721s Warning: skipping mate #2 of read '94' because it was < 2 characters long 721s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '96' because it was < 2 characters long 721s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '98' because it was < 2 characters long 721s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '101' because it was < 2 characters long 721s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '104' because it was < 2 characters long 721s Warning: skipping mate #1 of read '108' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '108' because it was < 2 characters long 721s Warning: skipping mate #2 of read '112' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read '112' because it was < 2 characters long 721s Warning: skipping mate #1 of read '114' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #1 of read '114' because it was < 2 characters long 721s 120 reads; of these: 721s 105 (diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 721s 87.50%) were paired; of these: 721s 105 (100.00%) aligned concordantly 0 times 721s 0 (0.00%) aligned concordantly exactly 1 time 721s 0 (0.00%) aligned concordantly >1 times 721s ---- 721s 105 pairs aligned concordantly 0 times; of these: 721s 0 (0.00%) aligned discordantly 1 time 721s ---- 721s 105 pairs aligned 0 times concordantly or discordantly; of these: 721s 210 mates make up the pairs; of these: 721s 210 (100.00%) aligned 0 times 721s 0 (0.00%) aligned exactly 1 time 721s 0 (0.00%) aligned >1 times 721s 15 (12.50%) were unpaired; of these: 721s 15 (100.00%) aligned 0 times 721s 0 (0.00%) aligned exactly 1 time 721s 0 (0.00%) aligned >1 times 721s 0.00% overall alignment rate 721s Flattened IUPAC characters 721s Mutating sequence Sim.pm.2 721s Introducing 2 SNPs, 1/1 ref/read gaps, and 2 rearrangements 721s Finished SNPs 721s Finished ref gaps 721s Finished read gaps 721s Mutating sequence Sim.pm.1 721s Introducing 10 SNPs, 0/1 ref/read gaps, and 3 rearrangements 721s Finished SNPs 721s Finished ref gaps 721s Finished read gaps 721s Mutated reference genome to subject genome 721s SNPs introduced: 12 721s Reference gaps introduced: 1 721s Read gaps introduced: 2 721s Rearrangements introduced: 5 721s Created read sampler 721s Sampling 118 reads 721s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 721s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 721s parsing sequence Sim.pm.1... 721s *** Run 44 of 100 721s /usr/bin/bowtie2 -i L,0.0821346712677959 --nofw --rfg 11.1276729213317 --cp-ival 4 --local -k 3 -D 4 --score-min L,3.05621665333324,1.04829441574636 --mm --large-index --np 5 --cp-min 2 --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq 721s parsing sequence Sim.pm.2... 721s Parsed 40 reference bases 721s Warning: skipping mate #2 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 721s Read 50 alignments... 721s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 721s Warning: skipping mate #2 of read 'R_1_1_1_85_85_1/1' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 721s Read 100 alignments... 721s Read 150 alignments... 721s 118 reads; of these: 721s 118 (100.00%) were paired; of these: 721s 118 (100.00%) aligned concordantly 0 times 721s 0 (0.00%) aligned concordantly exactly 1 time 721s 0 (0.00%) aligned concordantly >1 times 721s ---- 721s 118 pairs aligned concordantly 0 times; of these: 721s 0 (0.00%) aligned discordantly 1 time 721s /usr/bin/bowtie2 -i L,0.0821346712677959 --nofw --rfg 11.1276729213317 --cp-ival 4 --local -k 3 -D 4 --score-min L,3.05621665333324,1.04829441574636 --mm --large-index --np 5 --cp-min 2 --qseq -p 2 -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 721s ---- 721s 118 pairs aligned 0 times concordantly or discordantly; of these: 721s 236 mates make up the pairs; of these: 721s 226 (95.76%) aligned 0 times 721s 7 (2.97%) aligned exactly 1 time 721s 3 (1.27%) aligned >1 times 721s 4.24% overall alignment rate 721s Read 200 alignments... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s ACATCTTCG 721s ACATCTTCG 721s Processing line... 721s Processing line... 721s GGGG 721s GGGG 721s Processing line... 721s GGGG 721s GGGG 721s Processing line... 721s Processing line... 721s GAGGAGGAG 721s GAGGAGGAG 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s ACATCTTCG 721s ACATCTTCG 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s CGAGGAGGA 721s CGAGGAGGA 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s GGA 721s GGA 721s Processing line... 721s GGA 721s GGA 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s CTTCGCG 721s CTTCGCG 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s CATCTTCGCGAGGA 721s CATCTTCGCGAGGA 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s ACGG 721s ACGG 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s CGC 721s CGC 721s Processing line... 721s CGC 721s CGC 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s Processing line... 721s --- Summary --- 721s Read 1 reference strings 721s Checked 13 alignments, 0 edits 721s --------------- 721s PASSED 721s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 721s Warning: skipping mate #2 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 721s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 721s Warning: skipping mate #2 of read 'R_1_1_1_85_85_1/1' because length (1) <= # seed mismatches (0) 721s Warning: skipping mate #2 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 721s 118 reads; of these: 721s 118 (100.00%) were paired; of these: 721s 118 (100.00%) aligned concordantly 0 times 721s 0 (0.00%) aligned concordantly exactly 1 time 721s 0 (0.00%) aligned concordantly >1 times 721s ---- 721s 118 pairs aligned concordantly 0 times; of these: 721s 0 (0.00%) aligned discordantly 1 time 721s ---- 721s 118 pairs aligned 0 times concordantly or discordantly; of these: 721s 236 mates make up the pairs; of these: 721s 226 (95.76%) aligned 0 times 721s 7 (2.97%) aligned exactly 1 time 721s 3 (1.27%) aligned >1 times 721s 4.24% overall alignment rate 721s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 721s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 721s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 721s Flattened IUPAC characters 721s Mutating sequence Sim.pm.1 721s Introducing 12 SNPs, 0/0 ref/read gaps, and 3 rearrangements 721s Finished SNPs 721s Finished ref gaps 721s Finished read gaps 721s Mutating sequence Sim.pm.2 721s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 721s Finished SNPs 721s Finished ref gaps 721s Finished read gaps 721s Mutated reference genome to subject genome 721s SNPs introduced: 16 721s Reference gaps introduced: 0 721s Read gaps introduced: 1 721s Rearrangements introduced: 3 721s Created read sampler 721s Sampling 89 reads 721s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 721s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 721s *** Run 45 of 100 721s /usr/bin/bowtie2 --ma 4.66783122660856 --score-min L,2.84873004590257,3.12619778175224 -R 4 --rdg 8.83123756742813 --cp-min 2 --np 2 --large-index --nofw --trim3 3 --mp 9.76167603849548,1.05918766326781 --rfg 5.16014817897817 -M 3 --trim5 0 --cp-ival 1 -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta 721s parsing sequence Sim.pm.1... 721s parsing sequence Sim.pm.2... 721s Parsed 40 reference bases 721s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 721s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 721s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 721s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '11' because it was < 2 characters long 721s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 721s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '20' because it was < 2 characters long 721s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 721s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '26' because it was < 2 characters long 721s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 721s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '30' because it was < 2 characters long 721s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 721s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 721s Warning: skipping read '35' because it was < 2 characters long 721s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 721s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '40' because it was < 2 characters long 721s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 721s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 721s Warning: skipping read '50' because it was < 2 characters long 721s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 721s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '58' because it was < 2 characters long 721s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 721s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 721s Warning: skipping read '61' because it was < 2 characters long 721s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 721s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 721s Warning: skipping read '78' because it was < 2 characters long 721s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 721s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 722s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 722s Warning: skipping read '84' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 722s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 722s Warning: skipping read '87' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 722s /usr/bin/bowtie2 --ma 4.66783122660856 --score-min L,2.84873004590257,3.12619778175224 -R 4 --rdg 8.83123756742813 --cp-min 2 --np 2 --large-index --nofw --trim3 3 --mp 9.76167603849548,1.05918766326781 --rfg 5.16014817897817 -M 3 --trim5 0 --cp-ival 1 -f -p 4 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 722s 89 reads; of these: 722s 89 (100.00%) were unpaired; of these: 722s 88 (98.88%) aligned 0 times 722s 0 (0.00%) aligned exactly 1 time 722s 1 (1.12%) aligned >1 times 722s 1.12% overall alignment rate 722s Read 50 alignments... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s CGA 722s CGA 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s --- Summary --- 722s Read 1 reference strings 722s Checked 1 alignments, 0 edits 722s --------------- 722s PASSED 722s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 722s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 722s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 722s Warning: skipping read '11' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 722s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 722s Warning: skipping read '20' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 722s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 722s Warning: skipping read '26' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 722s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 722s Warning: skipping read '30' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 722s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 722s Warning: skipping read '35' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 722s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 722s Warning: skipping read '40' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 722s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 722s Warning: skipping read '50' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 722s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 722s Warning: skipping read '58' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 722s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 722s Warning: skipping read '61' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 722s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 722s Warning: skipping read '78' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 722s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 722s Warning: skipping read '84' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 722s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 722s Warning: skipping read '87' because it was < 2 characters long 722s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 722s 89 reads; of these: 722s 89 (100.00%) were unpaired; of these: 722s 88 (98.88%) aligned 0 times 722s 0 (0.00%) aligned exactly 1 time 722s 1 (1.12%) aligned >1 times 722s 1.12% overall alignment rate 722s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 722s Flattened IUPAC characters 722s Mutating sequence Sim.pm.1 722s Introducing 1 SNPs, 3/1 ref/read gaps, and 2 rearrangements 722s Finished SNPs 722s Finished ref gaps 722s Finished read gaps 722s Mutating sequence Sim.pm.2 722s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 722s Finished SNPs 722s Finished ref gaps 722s Finished read gaps 722s Mutated reference genome to subject genome 722s SNPs introduced: 2 722s Reference gaps introduced: 3 722s Read gaps introduced: 1 722s Rearrangements introduced: 2 722s Created read sampler 722s Sampling 2 reads 722s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 722s *** Run 46 of 100 722s /usr/bin/bowtie2 --mm --score-min L,9.26424541206139,7.79758437108 --trim3 7 --local --cp-ival 2 --large-index -M 3 --cp-min 5 --n-ceil 0.163146601229655,0.794699198356565 --trim5 1 --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq 722s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 722s parsing sequence Sim.pm.1... 722s parsing sequence Sim.pm.2... 722s Parsed 40 reference bases 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s 2 reads; of these: 722s 2 (100.00%) were paired; of these: 722s 2 (100.00%) aligned concordantly 0 times 722s 0 (0.00%) aligned concordantly exactly 1 time 722s 0 (0.00%) aligned concordantly >1 times 722s ---- 722s 2 pairs aligned concordantly 0 times; of these: 722s 0 (0.00%) aligned discordantly 1 time 722s ---- 722s 2 pairs aligned 0 times concordantly or discordantly; of these: 722s 4 mates make up the pairs; of these: 722s 4 (100.00%) aligned 0 times 722s 0 (0.00%) aligned exactly 1 time 722s 0 (0.00%) aligned >1 times 722s 0.00% overall alignment rate 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s --- Summary --- 722s Read 1 reference strings 722s Checked 0 alignments, 0 edits 722s --------------- 722s PASSED 722s Flattened IUPAC characters 722s Mutating sequence Sim.pm.1 722s Introducing 10 SNPs, 1/1 ref/read gaps, and 0 rearrangements 722s Finished SNPs 722s Finished ref gaps 722s Finished read gaps 722s *** Run 47 of 100 722s /usr/bin/bowtie2 -D 35 -k 4 --gbar 6 --score-min L,1.64844197133443,6.97287033623735 --cp-min 2 --np 5 --large-index --rfg 18.9223291475316,12.3131547209891 --mp 6.42922678053578,6.09032119236761 -N 1 -L25 --trim3 3 --cp-ival 2 --local --n-ceil 0.590946851871201,0.745530934943878 --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq 722s Mutating sequence Sim.pm.2 722s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 722s Finished SNPs 722s Finished ref gaps 722s Finished read gaps 722s Mutated reference genome to subject genome 722s SNPs introduced: 10 722s Reference gaps introduced: 1 722s Read gaps introduced: 1 722s Rearrangements introduced: 0 722s Created read sampler 722s Sampling 116 reads 722s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 722s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 722s parsing sequence Sim.pm.1... 722s parsing sequence Sim.pm.2... 722s Parsed 40 reference bases 722s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 722s 116 reads; of these: 722s 116 (100.00%) were unpaired; of these: 722s 116 (100.00%) aligned 0 times 722s 0 (0.00%) aligned exactly 1 time 722s 0 (0.00%) aligned >1 times 722s 0.00% overall alignment rate 722s Read 50 alignments... 722s Read 100 alignments... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s --- Summary --- 722s Read 1 reference strings 722s Checked 0 alignments, 0 edits 722s --------------- 722s PASSED 722s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 722s /usr/bin/bowtie2 -D 35 -k 4 --gbar 6 --score-min L,1.64844197133443,6.97287033623735 --cp-min 2 --np 5 --large-index --rfg 18.9223291475316,12.3131547209891 --mp 6.42922678053578,6.09032119236761 -N 1 -L25 --trim3 3 --cp-ival 2 --local --n-ceil 0.590946851871201,0.745530934943878 --qseq -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 722s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 722s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (1) 722s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 722s 116 reads; of these: 722s 116 (100.00%) were unpaired; of these: 722s 116 (100.00%) aligned 0 times 722s 0 (0.00%) aligned exactly 1 time 722s 0 (0.00%) aligned >1 times 722s 0.00% overall alignment rate 722s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 722s Flattened IUPAC characters 722s Mutating sequence Sim.pm.2 722s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 722s Finished SNPs 722s Finished ref gaps 722s Finished read gaps 722s Mutating sequence Sim.pm.1 722s Introducing 7 SNPs, 0/2 ref/read gaps, and 2 rearrangements 722s Finished SNPs 722s Finished ref gaps 722s Finished read gaps 722s Mutated reference genome to subject genome 722s SNPs introduced: 11 722s Reference gaps introduced: 0 722s Read gaps introduced: 3 722s Rearrangements introduced: 2 722s Created read sampler 722s Sampling 104 reads 722s *** Run 48 of 100 722s /usr/bin/bowtie2 --np 3 --cp-min 7 --large-index --score-min L,1.67323428402884,2.50057107096004 -D 43 --rdg 29.0742119505573 -M 5 --local --cp-ival 1 --nofw --mp 5.47214515140855,1.74186678093796 --rfg 6.7072801339062 -r -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.raw -2 /tmp/Sim.pm.qtk7xXsv_2.raw 722s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 722s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 722s parsing sequence Sim.pm.1... 722s parsing sequence Sim.pm.2... 722s Parsed 40 reference bases 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 722s Warning: skipping mate #2 of read '16' because it was < 2 characters long 722s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 722s Warning: skipping mate #2 of read '21' because it was < 2 characters long 722s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 722s Warning: skipping mate #1 of read '42' because it was < 2 characters long 722s Warning: skipping mate #1 of read '61' because length (1) <= # seed mismatches (0) 722s Warning: skipping mate #1 of read '61' because it was < 2 characters long 722s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 722s Warning: skipping mate #2 of read '63' because it was < 2 characters long 722s Warning: skipping mate #1 of read '71' because length (1) <= # seed mismatches (0) 722s Warning: skipping mate #1 of read '71' because it was < 2 characters long 722s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (0) 722s Warning: skipping mate #2 of read '91' because it was < 2 characters long 722s Read 50 alignments... 722s 104 reads; of these: 722s 104 (100.00%) were paired; of these: 722s 104 (100.00%) aligned concordantly 0 times 722s 0 (0.00%) aligned concordantly exactly 1 time 722s 0 (0.00%) aligned concordantly >1 times 722s ---- 722s 104 pairs aligned concordantly 0 times; of these: 722s 0 (0.00%) aligned discordantly 1 time 722s ---- 722s 104 pairs aligned 0 times concordantly or discordantly; of these: 722s 208 mates make up the pairs; of these: 722s 208 (100.00%) aligned 0 times 722s 0 (0.00%) aligned exactly 1 time 722s 0 (0.00%) aligned >1 times 722s 0.00% overall alignment rate 722s Read 100 alignments... 722s Read 150 alignments... 722s Read 200 alignments... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s --- Summary --- 722s Read 1 reference strings 722s Checked 0 alignments, 0 edits 722s --------------- 722s PASSED 722s Flattened IUPAC characters 722s Mutating sequence Sim.pm.2 722s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 722s Finished SNPs 722s Finished ref gaps 722s Finished read gaps 722s Mutating sequence Sim.pm.1 722s Introducing 25 SNPs, 2/0 ref/read gaps, and 2 rearrangements 722s Finished SNPs 722s Finished ref gaps 722s Finished read gaps 722s Mutated reference genome to subject genome 722s SNPs introduced: 28 722s Reference gaps introduced: 3 722s Read gaps introduced: 0 722s Rearrangements introduced: 3 722s Created read sampler 722s Sampling 16 reads 722s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 722s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 722s parsing sequence Sim.pm.1... 722s parsing sequence Sim.pm.2... 722s Parsed 40 reference bases 722s *** Run 49 of 100 722s /usr/bin/bowtie2 --mm -R 3 -D 23 --score-min L,6.69499557515356,6.88530927582238 --np 3 --cp-min 8 --large-index -i L,0.0924197751356666 --mp 7.03383021889048,5.80853319714094 --cp-ival 1 --n-ceil 0.677400626511804,0.915599611041121 -M 7 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 722s 16 reads; of these: 722s 16 (100.00%) were unpaired; of these: 722s 13 (81.25%) aligned 0 times 722s 1 (6.25%) aligned exactly 1 time 722s 2 (12.50%) aligned >1 times 722s 18.75% overall alignment rate 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s GC 722s GC 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s CGG 722s CGG 722s Processing line... 722s Processing line... 722s Processing line... 722s Processing line... 722s GCCGGGGGCCTGC 722s GCCGGGGGCCTGC 722s Processing line... 722s Processing line... 722s Processing line... 722s --- Summary --- 722s Read 1 reference strings 722s Checked 3 alignments, 0 edits 722s --------------- 722s PASSED 722s ALSO checking that bowtie2 and bowtie2-align match up 722s /usr/bin/bowtie2 --mm -R 3 -D 23 --score-min L,6.69499557515356,6.88530927582238 --np 3 --cp-min 8 --large-index -i L,0.0924197751356666 --mp 7.03383021889048,5.80853319714094 --cp-ival 1 --n-ceil 0.677400626511804,0.915599611041121 -M 7 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 722s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 722s 16 reads; of these: 722s 16 (100.00%) were unpaired; of these: 722s 13 (81.25%) aligned 0 times 722s 1 (6.25%) aligned exactly 1 time 722s 2 (12.50%) aligned >1 times 722s 18.75% overall alignment rate 722s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 722s Flattened IUPAC characters 722s Mutating sequence Sim.pm.1 722s Introducing 13 SNPs, 1/1 ref/read gaps, and 1 rearrangements 722s Finished SNPs 722s Finished ref gaps 722s Finished read gaps 722s Mutating sequence Sim.pm.2 722s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 722s Finished SNPs 722s Finished ref gaps 722s Finished read gaps 722s Mutated reference genome to subject genome 722s SNPs introduced: 16 722s Reference gaps introduced: 1 722s Read gaps introduced: 2 722s Rearrangements introduced: 1 722s Created read sampler 722s Sampling 120 reads 722s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 722s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 722s parsing sequence Sim.pm.1... 722s parsing sequence Sim.pm.2... 722s Parsed 40 reference bases 722s *** Run 50 of 100 722s /usr/bin/bowtie2 --trim3 0 --rfg 40.6521980866961,13.0238473527259 -a --trim5 2 --local --cp-ival 2 --score-min L,8.66407735852831,9.5730335175562 --cp-min 2 --np 2 --large-index -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq 723s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '1' because it was < 2 characters long 723s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 723s Warning: skipping mate #2 of read '14' because it was < 2 characters long 723s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '23' because it was < 2 characters long 723s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '24' because it was < 2 characters long 723s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '26' because it was < 2 characters long 723s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '49' because it was < 2 characters long 723s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '52' because it was < 2 characters long 723s Warning: skipping mate #1 of read '61' because length (1) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '61' because it was < 2 characters long 723s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '64' because it was < 2 characters long 723s Read 50 alignments... 723s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '82' because it was < 2 characters long 723s Warning: skipping mate #1 of read '118' because length (1) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '118' because it was < 2 characters long 723s Read 100 alignments... 723s Read 150 alignments... 723s Read 200 alignments... 723s 120 reads; of these: 723s 114 (95.00%) were paired; of these: 723s 114 (100.00%) aligned concordantly 0 times 723s 0 (0.00%) aligned concordantly exactly 1 time 723s 0 (0.00%) aligned concordantly >1 times 723s ---- 723s 114 pairs aligned concordantly 0 times; of these: 723s 0 (0.00%) aligned discordantly 1 time 723s ---- 723s 114 pairs aligned 0 times concordantly or discordantly; of these: 723s 228 mates make up the pairs; of these: 723s 228 (100.00%) aligned 0 times 723s 0 (0.00%) aligned exactly 1 time 723s 0 (0.00%) aligned >1 times 723s 6 (5.00%) were unpaired; of these: 723s 6 (100.00%) aligned 0 times 723s 0 (0.00%) aligned exactly 1 time 723s 0 (0.00%) aligned >1 times 723s 0.00% overall alignment rate 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing 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line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s --- Summary --- 723s Read 1 reference strings 723s Checked 0 alignments, 0 edits 723s --------------- 723s PASSED 723s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 723s /usr/bin/bowtie2 --trim3 0 --rfg 40.6521980866961,13.0238473527259 -a --trim5 2 --local --cp-ival 2 --score-min L,8.66407735852831,9.5730335175562 --cp-min 2 --np 2 --large-index -q -p 4 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 723s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '1' because it was < 2 characters long 723s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 723s Warning: skipping mate #2 of read '14' because it was < 2 characters long 723s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '23' because it was < 2 characters long 723s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '24' because it was < 2 characters long 723s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '26' because it was < 2 characters long 723s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '49' because it was < 2 characters long 723s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '52' because it was < 2 characters long 723s Warning: skipping mate #1 of read '61' because length (1) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '61' because it was < 2 characters long 723s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '64' because it was < 2 characters long 723s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '82' because it was < 2 characters long 723s Warning: skipping mate #1 of read '118' because length (1) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read '118' because it was < 2 characters long 723s 120 reads; of these: 723s 114 (95.00%) were paired; of these: 723s 114 (100.00%) aligned concordantly 0 times 723s 0 (0.00%) aligned concordantly exactly 1 time 723s 0 (0.00%) aligned concordantly >1 times 723s ---- 723s 114 pairs aligned concordantly 0 times; of these: 723s 0 (0.00%) aligned discordantly 1 time 723s ---- 723s 114 pairs aligned 0 times concordantly or discordantly; of these: 723s 228 mates make up the pairs; of these: 723s 228 (100.00%) aligned 0 times 723s 0 (0.00%) aligned exactly 1 time 723s 0 (0.00%) aligned >1 times 723s 6 (5.00%) were unpaired; of these: 723s 6 (100.00%) aligned 0 times 723s 0 (0.00%) aligned exactly 1 time 723s 0 (0.00%) aligned >1 times 723s 0.00% overall alignment rate 723s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 723s Flattened IUPAC characters 723s Mutating sequence Sim.pm.2 723s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 723s Finished SNPs 723s Finished ref gaps 723s Finished read gaps 723s Mutating sequence Sim.pm.1 723s Introducing 6 SNPs, 1/1 ref/read gaps, and 1 rearrangements 723s Finished SNPs 723s Finished ref gaps 723s Finished read gaps 723s Mutated reference genome to subject genome 723s SNPs introduced: 6 723s Reference gaps introduced: 1 723s Read gaps introduced: 1 723s Rearrangements introduced: 1 723s *** Run 51 of 100 723s /usr/bin/bowtie2 --large-index --cp-min 3 --cp-ival 1 --score-min L,2.52307050976017,3.66880429063382 --trim3 5 --ma 39.3560138499649 --gbar 1 -R 3 --mp 9.28771638891469,1.74954607557106 --rdg 21.7926675041098 --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq 723s Created read sampler 723s Sampling 35 reads 723s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 723s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 723s parsing sequence Sim.pm.1... 723s parsing sequence Sim.pm.2... 723s Parsed 40 reference bases 723s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 723s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 723s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 723s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 723s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 723s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 723s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 723s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 723s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 723s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 723s 35 reads; of these: 723s 32 (91.43%) were paired; of these: 723s 32 (100.00%) aligned concordantly 0 times 723s 0 (0.00%) aligned concordantly exactly 1 time 723s 0 (0.00%) aligned concordantly >1 times 723s ---- 723s 32 pairs aligned concordantly 0 times; of these: 723s 0 (0.00%) aligned discordantly 1 time 723s ---- 723s 32 pairs aligned 0 times concordantly or discordantly; of these: 723s 64 mates make up the pairs; of these: 723s 64 (100.00%) aligned 0 times 723s 0 (0.00%) aligned exactly 1 time 723s 0 (0.00%) aligned >1 times 723s 3 (8.57%) were unpaired; of these: 723s 3 (100.00%) aligned 0 times 723s 0 (0.00%) aligned exactly 1 time 723s 0 (0.00%) aligned >1 times 723s 0.00% overall alignment rate 723s Read 50 alignments... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s --- Summary --- 723s Read 1 reference strings 723s Checked 0 alignments, 0 edits 723s --------------- 723s PASSED 723s Flattened IUPAC characters 723s Mutating sequence Sim.pm.2 723s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 723s Finished SNPs 723s Finished ref gaps 723s Finished read gaps 723s Mutating sequence Sim.pm.1 723s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 723s Finished SNPs 723s Finished ref gaps 723s Finished read gaps 723s Mutated reference genome to subject genome 723s SNPs introduced: 5 723s Reference gaps introduced: 0 723s Read gaps introduced: 1 723s Rearrangements introduced: 1 723s Created read sampler 723s Sampling 118 reads 723s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 723s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 723s parsing sequence Sim.pm.1... 723s parsing sequence Sim.pm.2... 723s Parsed 40 reference bases 723s *** Run 52 of 100 723s /usr/bin/bowtie2 --rfg 16.5096524685251,12.5291254944055 -N 1 -i C,2.33529157168222 --score-min L,6.61565847384323,3.90355313979183 --cp-ival 3 --local --trim5 5 --cp-min 4 -a --large-index -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 723s Warning: skipping read '0' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '0' because it was < 2 characters long 723s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '4' because it was < 2 characters long 723s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '7' because it was < 2 characters long 723s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '14' because it was < 2 characters long 723s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '18' because it was < 2 characters long 723s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '28' because it was < 2 characters long 723s Warning: skipping read '35' because length (1) <= # seed mismatches (1) 723s Warning: skipping read '35' because it was < 2 characters long 723s Warning: skipping read '39' because length (1) <= # seed mismatches (1) 723s Warning: skipping read '39' because it was < 2 characters long 723s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '41' because it was < 2 characters long 723s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '54' because it was < 2 characters long 723s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '59' because it was < 2 characters long 723s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '73' because it was < 2 characters long 723s Warning: skipping read '74' because length (1) <= # seed mismatches (1) 723s Warning: skipping read '74' because it was < 2 characters long 723s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '81' because it was < 2 characters long 723s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '83' because it was < 2 characters long 723s Warning: skipping read '89' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '89' because it was < 2 characters long 723s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '99' because it was < 2 characters long 723s Warning: skipping read '100' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '100' because it was < 2 characters long 723s Warning: skipping read '105' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '105' because it was < 2 characters long 723s Warning: skipping read '107' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '107' because it was < 2 characters long 723s 118 reads; of these: 723s 118 (100.00%) were unpaired; of these: 723s 118 (100.00%) aligned 0 times 723s 0 (0.00%) aligned exactly 1 time 723s 0 (0.00%) aligned >1 times 723s 0.00% overall alignment rate 723s Read 50 alignments... 723s Read 100 alignments... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s Processing line... 723s /usr/bin/bowtie2 --rfg 16.5096524685251,12.5291254944055 -N 1 -i C,2.33529157168222 --score-min L,6.61565847384323,3.90355313979183 --cp-ival 3 --local --trim5 5 --cp-min 4 -a --large-index -r -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 723s Processing line... 723s Processing line... 723s Processing line... 723s --- Summary --- 723s Read 1 reference strings 723s Checked 0 alignments, 0 edits 723s --------------- 723s PASSED 723s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 723s Warning: skipping read '0' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '0' because it was < 2 characters long 723s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '4' because it was < 2 characters long 723s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '7' because it was < 2 characters long 723s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '14' because it was < 2 characters long 723s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '18' because it was < 2 characters long 723s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '28' because it was < 2 characters long 723s Warning: skipping read '35' because length (1) <= # seed mismatches (1) 723s Warning: skipping read '35' because it was < 2 characters long 723s Warning: skipping read '39' because length (1) <= # seed mismatches (1) 723s Warning: skipping read '39' because it was < 2 characters long 723s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '41' because it was < 2 characters long 723s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '54' because it was < 2 characters long 723s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '59' because it was < 2 characters long 723s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '73' because it was < 2 characters long 723s Warning: skipping read '74' because length (1) <= # seed mismatches (1) 723s Warning: skipping read '74' because it was < 2 characters long 723s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '81' because it was < 2 characters long 723s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '83' because it was < 2 characters long 723s Warning: skipping read '89' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '89' because it was < 2 characters long 723s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '99' because it was < 2 characters long 723s Warning: skipping read '100' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '100' because it was < 2 characters long 723s Warning: skipping read '105' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '105' because it was < 2 characters long 723s Warning: skipping read '107' because length (0) <= # seed mismatches (1) 723s Warning: skipping read '107' because it was < 2 characters long 723s 118 reads; of these: 723s 118 (100.00%) were unpaired; of these: 723s 118 (100.00%) aligned 0 times 723s 0 (0.00%) aligned exactly 1 time 723s 0 (0.00%) aligned >1 times 723s 0.00% overall alignment rate 723s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 723s Flattened IUPAC characters 723s Mutating sequence Sim.pm.1 723s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 723s Finished SNPs 723s Finished ref gaps 723s Finished read gaps 723s Mutating sequence Sim.pm.2 723s Introducing 3 SNPs, 0/1 ref/read gaps, and 1 rearrangements 723s Finished SNPs 723s Finished ref gaps 723s Finished read gaps 723s Mutated reference genome to subject genome 723s SNPs introduced: 11 723s Reference gaps introduced: 0 723s Read gaps introduced: 1 723s Rearrangements introduced: 2 723s Created read sampler 723s Sampling 59 reads 723s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 723s *** Run 53 of 100 723s /usr/bin/bowtie2 --rdg 28.8133565886576,4.4256207841345 --rfg 29.7077038130513,3.91222216772795 --score-min L,6.83716861352293,9.97207410429898 -D 3 --local --cp-ival 1 --large-index --cp-min 2 --n-ceil 0.897427491974708,1.21215601173847 --trim5 1 -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta 723s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 723s parsing sequence Sim.pm.1... 723s parsing sequence Sim.pm.2... 723s Parsed 40 reference bases 723s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 723s Warning: skipping read '5' because it was < 2 characters long 723s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 723s Warning: skipping read '34' because it was < 2 characters long 723s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 723s Warning: skipping read '36' because it was < 2 characters long 723s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 723s Warning: skipping read '39' because it was < 2 characters long 723s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 723s Warning: skipping read '43' because it was < 2 characters long 723s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 723s Warning: skipping read '57' because it was < 2 characters long 724s 59 reads; of these: 724s 59 (100.00%) were unpaired; of these: 724s 59 (100.00%) aligned 0 times 724s 0 (0.00%) aligned exactly 1 time 724s 0 (0.00%) aligned >1 times 724s 0.00% overall alignment rate 724s Read 50 alignments... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s /usr/bin/bowtie2 --rdg 28.8133565886576,4.4256207841345 --rfg 29.7077038130513,3.91222216772795 --score-min L,6.83716861352293,9.97207410429898 -D 3 --local --cp-ival 1 --large-index --cp-min 2 --n-ceil 0.897427491974708,1.21215601173847 --trim5 1 -f -p 4 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s --- Summary --- 724s Read 1 reference strings 724s Checked 0 alignments, 0 edits 724s --------------- 724s PASSED 724s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 724s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '5' because it was < 2 characters long 724s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '34' because it was < 2 characters long 724s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '36' because it was < 2 characters long 724s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '39' because it was < 2 characters long 724s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 724s Warning: skipping read '43' because it was < 2 characters long 724s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 724s Warning: skipping read '57' because it was < 2 characters long 724s 59 reads; of these: 724s 59 (100.00%) were unpaired; of these: 724s 59 (100.00%) aligned 0 times 724s 0 (0.00%) aligned exactly 1 time 724s 0 (0.00%) aligned >1 times 724s 0.00% overall alignment rate 724s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 724s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 724s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 724s /usr/bin/bowtie2 --rdg 28.8133565886576,4.4256207841345 --rfg 29.7077038130513,3.91222216772795 --score-min L,6.83716861352293,9.97207410429898 -D 3 --local --cp-ival 1 --large-index --cp-min 2 --n-ceil 0.897427491974708,1.21215601173847 --trim5 1 -f -p 3 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 724s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 724s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '5' because it was < 2 characters long 724s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '34' because it was < 2 characters long 724s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '36' because it was < 2 characters long 724s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '39' because it was < 2 characters long 724s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 724s Warning: skipping read '43' because it was < 2 characters long 724s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 724s Warning: skipping read '57' because it was < 2 characters long 724s 59 reads; of these: 724s 59 (100.00%) were unpaired; of these: 724s 59 (100.00%) aligned 0 times 724s 0 (0.00%) aligned exactly 1 time 724s 0 (0.00%) aligned >1 times 724s 0.00% overall alignment rate 724s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 724s Flattened IUPAC characters 724s Mutating sequence Sim.pm.2 724s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 724s Finished SNPs 724s Finished ref gaps 724s Finished read gaps 724s Mutating sequence Sim.pm.1 724s Introducing 26 SNPs, 0/0 ref/read gaps, and 1 rearrangements 724s Finished SNPs 724s Finished ref gaps 724s Finished read gaps 724s Mutated reference genome to subject genome 724s SNPs introduced: 26 724s Reference gaps introduced: 0 724s Read gaps introduced: 0 724s Rearrangements introduced: 1 724s Created read sampler 724s Sampling 9 reads 724s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 724s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 724s *** Run 54 of 100 724s /usr/bin/bowtie2 --mm --gbar 4 --score-min L,1.96781325678533,5.74393016623057 --large-index --cp-min 6 --np 6 --rfg 28.1819509670445 --nofw --trim3 1 --cp-ival 1 --local --trim5 8 --norc -a -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 724s parsing sequence Sim.pm.1... 724s parsing sequence Sim.pm.2... 724s Parsed 40 reference bases 724s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 724s Warning: skipping mate #1 of read '4' because it was < 2 characters long 724s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 724s Warning: skipping mate #1 of read '9' because it was < 2 characters long 724s 9 reads; of these: 724s 8 (88.89%) were paired; of these: 724s 8 (100.00%) aligned concordantly 0 times 724s 0 (0.00%) aligned concordantly exactly 1 time 724s 0 (0.00%) aligned concordantly >1 times 724s ---- 724s 8 pairs aligned concordantly 0 times; of these: 724s 0 (0.00%) aligned discordantly 1 time 724s ---- 724s 8 pairs aligned 0 times concordantly or discordantly; of these: 724s 16 mates make up the pairs; of these: 724s 16 (100.00%) aligned 0 times 724s 0 (0.00%) aligned exactly 1 time 724s 0 (0.00%) aligned >1 times 724s 1 (11.11%) were unpaired; of these: 724s 1 (100.00%) aligned 0 times 724s 0 (0.00%) aligned exactly 1 time 724s 0 (0.00%) aligned >1 times 724s 0.00% overall alignment rate 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s --- Summary --- 724s Read 1 reference strings 724s Checked 0 alignments, 0 edits 724s --------------- 724s PASSED 724s Flattened IUPAC characters 724s Mutating sequence Sim.pm.1 724s Introducing 17 SNPs, 3/3 ref/read gaps, and 3 rearrangements 724s Finished SNPs 724s Finished ref gaps 724s Finished read gaps 724s Mutating sequence Sim.pm.2 724s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 724s Finished SNPs 724s Finished ref gaps 724s Finished read gaps 724s Mutated reference genome to subject genome 724s SNPs introduced: 19 724s Reference gaps introduced: 4 724s Read gaps introduced: 3 724s Rearrangements introduced: 3 724s Created read sampler 724s Sampling 164 reads 724s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 724s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 724s parsing sequence Sim.pm.1... 724s parsing sequence Sim.pm.2... 724s Parsed 40 reference bases 724s *** Run 55 of 100 724s /usr/bin/bowtie2 -i S,1.04459450477293 -N 0 -L13 --mp 4.30946501405189,2.27579909676822 --trim3 5 --rfg 40.001558306223 --trim5 2 --cp-ival 1 -R 3 -k 2 -D 21 --score-min L,7.18400857860257,9.44816641513917 --cp-min 3 --np 5 --large-index -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 724s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 724s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '3' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 724s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '16' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 724s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '17' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 724s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '32' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 724s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '33' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 724s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '39' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 724s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '40' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 724s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 724s Warning: skipping read '44' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 724s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '48' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 724s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '56' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 724s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '60' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 724s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '61' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 724s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '64' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 724s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '70' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 724s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '73' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 724s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '75' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 724s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '77' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 724s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '79' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 724s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '85' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 724s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '86' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 724s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '90' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 724s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 724s Warning: skipping read '93' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 724s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '95' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 724s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '96' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 724s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '97' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 724s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '101' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 724s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '106' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 724s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '113' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 724s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '120' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 724s Warning: skipping read '141' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '141' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 724s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '143' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 724s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '144' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 724s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '147' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 724s Warning: skipping read '150' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '150' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 724s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '156' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 724s Warning: skipping read '157' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '157' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 724s Read 50 alignments... 724s 164 reads; of these: 724s 164 (100.00%) were unpaired; of these: 724s 155 (94.51%) aligned 0 times 724s 1 (0.61%) aligned exactly 1 time 724s 8 (4.88%) aligned >1 times 724s 5.49% overall alignment rate 724s Read 100 alignments... 724s Read 150 alignments... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s GGG 724s GGG 724s Processing line... 724s GGG 724s GGG 724s Processing line... 724s Processing line... 724s Processing line... 724s CT 724s CT 724s Processing line... 724s CT 724s CT 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s CGA 724s CGA 724s Processing line... 724s CGA 724s CGA 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s /usr/bin/bowtie2 -i S,1.04459450477293 -N 0 -L13 --mp 4.30946501405189,2.27579909676822 --trim3 5 --rfg 40.001558306223 --trim5 2 --cp-ival 1 -R 3 -k 2 -D 21 --score-min L,7.18400857860257,9.44816641513917 --cp-min 3 --np 5 --large-index -r -p 4 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s GG 724s GG 724s Processing line... 724s GG 724s GG 724s Processing line... 724s GCG 724s GCG 724s Processing line... 724s GCG 724s GCG 724s Processing line... 724s Processing line... 724s Processing line... 724s AGG 724s AGG 724s Processing line... 724s AGG 724s AGG 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s AGG 724s AGG 724s Processing line... 724s CCT 724s CCT 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s GA 724s GA 724s Processing line... 724s GA 724s GA 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s Processing line... 724s CGCGAGGAG 724s CGCGAGGAG 724s Processing line... 724s Processing line... 724s Processing line... 724s --- Summary --- 724s Read 1 reference strings 724s Checked 17 alignments, 0 edits 724s --------------- 724s PASSED 724s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 724s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 724s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '3' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 724s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '16' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 724s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '17' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 724s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '32' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 724s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '33' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 724s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '39' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 724s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '40' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 724s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 724s Warning: skipping read '44' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 724s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '48' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 724s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '56' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 724s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '60' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 724s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '61' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 724s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '64' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 724s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '70' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 724s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '73' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 724s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '75' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 724s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '77' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 724s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '79' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 724s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '85' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 724s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '86' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 724s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '90' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 724s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 724s Warning: skipping read '93' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 724s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '95' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 724s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '96' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 724s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '97' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 724s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '101' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 724s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '106' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 724s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '113' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 724s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '120' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 724s Warning: skipping read '141' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '141' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 724s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '143' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 724s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '144' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 724s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '147' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 724s Warning: skipping read '150' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '150' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 724s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '156' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 724s Warning: skipping read '157' because length (0) <= # seed mismatches (0) 724s Warning: skipping read '157' because it was < 2 characters long 724s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 724s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 724s 164 reads; of these: 724s 164 (100.00%) were unpaired; of these: 724s 155 (94.51%) aligned 0 times 724s 1 (0.61%) aligned exactly 1 time 724s 8 (4.88%) aligned >1 times 724s 5.49% overall alignment rate 724s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 724s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 724s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 724s Flattened IUPAC characters 724s Mutating sequence Sim.pm.2 724s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 724s Finished SNPs 724s Finished ref gaps 724s Finished read gaps 724s Mutating sequence Sim.pm.1 724s Introducing 9 SNPs, 1/0 ref/read gaps, and 3 rearrangements 724s Finished SNPs 724s Finished ref gaps 724s Finished read gaps 724s Mutated reference genome to subject genome 724s SNPs introduced: 9 724s Reference gaps introduced: 1 724s Read gaps introduced: 0 724s Rearrangements introduced: 3 724s Created read sampler 724s Sampling 101 reads 724s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 724s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 724s parsing sequence Sim.pm.1... 724s parsing sequence Sim.pm.2... 724s Parsed 40 reference bases 724s *** Run 56 of 100 724s /usr/bin/bowtie2 --large-index --cp-min 5 --trim5 2 --local --cp-ival 4 --score-min L,4.35755002051208,1.01040012337454 --trim3 6 -D 11 -i S,2.20087719898418,5.63326674039833 --rdg 23.2418880162577,12.8232302982242 -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 725s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '1' because it was < 2 characters long 725s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '2' because it was < 2 characters long 725s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '5' because it was < 2 characters long 725s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '8' because it was < 2 characters long 725s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '18' because it was < 2 characters long 725s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '19' because it was < 2 characters long 725s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '25' because it was < 2 characters long 725s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 725s Warning: skipping read '32' because it was < 2 characters long 725s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '35' because it was < 2 characters long 725s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '39' because it was < 2 characters long 725s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '41' because it was < 2 characters long 725s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '44' because it was < 2 characters long 725s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '47' because it was < 2 characters long 725s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '49' because it was < 2 characters long 725s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '54' because it was < 2 characters long 725s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '65' because it was < 2 characters long 725s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '73' because it was < 2 characters long 725s Read 50 alignments... 725s Read 100 alignments... 725s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '86' because it was < 2 characters long 725s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '90' because it was < 2 characters long 725s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '91' because it was < 2 characters long 725s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '96' because it was < 2 characters long 725s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '100' because it was < 2 characters long 725s 101 reads; of these: 725s 89 (88.12%) were paired; of these: 725s 89 (100.00%) aligned concordantly 0 times 725s 0 (0.00%) aligned concordantly exactly 1 time 725s 0 (0.00%) aligned concordantly >1 times 725s ---- 725s 89 pairs aligned concordantly 0 times; of these: 725s 0 (0.00%) aligned discordantly 1 time 725s ---- 725s 89 pairs aligned 0 times concordantly or discordantly; of these: 725s 178 mates make up the pairs; of these: 725s 171 (96.07%) aligned 0 times 725s 6 (3.37%) aligned exactly 1 time 725s 1 (0.56%) aligned >1 times 725s 12 (11.88%) were unpaired; of these: 725s 12 (100.00%) aligned 0 times 725s 0 (0.00%) aligned exactly 1 time 725s 0 (0.00%) aligned >1 times 725s 3.68% overall alignment rate 725s Read 150 alignments... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s AGGAG 725s AGGAG 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s ACATCTT 725s ACATCTT 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s TTCGC 725s TTCGC 725s Processing line... 725s Processing line... 725s ACATCTTCGC 725s ACATCTTCGC 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s ATCTTCGCGAGG 725s ATCTTCGCGAGG 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s CATCTTCGCGA 725s CATCTTCGCGA 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s ACATCTTCGCGAGGAGG 725s ACATCTTCGCGAGGAGG 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s --- Summary --- 725s Read 1 reference strings 725s Checked 7 alignments, 0 edits 725s --------------- 725s PASSED 725s Flattened IUPAC characters 725s Mutating sequence Sim.pm.1 725s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 725s Finished SNPs 725s Finished ref gaps 725s Finished read gaps 725s Mutating sequence Sim.pm.2 725s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 725s Finished SNPs 725s Finished ref gaps 725s Finished read gaps 725s Mutated reference genome to subject genome 725s SNPs introduced: 13 725s Reference gaps introduced: 0 725s Read gaps introduced: 0 725s Rearrangements introduced: 2 725s Created read sampler 725s Sampling 168 reads 725s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 725s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 725s parsing sequence Sim.pm.1... 725s parsing sequence Sim.pm.2... 725s Parsed 40 reference bases 725s *** Run 57 of 100 725s /usr/bin/bowtie2 --score-min L,4.64416137791877,2.01636748639459 --rdg 42.8338543916483,18.1679103357123 --mm --cp-min 3 --np 1 --large-index --trim3 2 -i S,0.648979152163131,2.77296013697126 --mp 3.15969744630823,2.90546432182401 --n-ceil 0.0494486129391622,1.31516672032381 --local --cp-ival 2 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 725s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '29' because it was < 2 characters long 725s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '57' because it was < 2 characters long 725s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 725s Warning: skipping read '58' because it was < 2 characters long 725s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '60' because it was < 2 characters long 725s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '74' because it was < 2 characters long 725s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 725s Warning: skipping read '88' because it was < 2 characters long 725s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '90' because it was < 2 characters long 725s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '95' because it was < 2 characters long 725s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '98' because it was < 2 characters long 725s Warning: skipping read '123' because length (1) <= # seed mismatches (0) 725s Warning: skipping read '123' because it was < 2 characters long 725s Warning: skipping read '157' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '157' because it was < 2 characters long 725s Read 50 alignments... 725s 168 reads; of these: 725s 168 (100.00%) were unpaired; of these: 725s 168 (100.00%) aligned 0 times 725s 0 (0.00%) aligned exactly 1 time 725s 0 (0.00%) aligned >1 times 725s 0.00% overall alignment rate 725s Read 100 alignments... 725s Read 150 alignments... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s --- Summary --- 725s Read 1 reference strings 725s Checked 0 alignments, 0 edits 725s /usr/bin/bowtie2 --score-min L,4.64416137791877,2.01636748639459 --rdg 42.8338543916483,18.1679103357123 --mm --cp-min 3 --np 1 --large-index --trim3 2 -i S,0.648979152163131,2.77296013697126 --mp 3.15969744630823,2.90546432182401 --n-ceil 0.0494486129391622,1.31516672032381 --local --cp-ival 2 -r -p 3 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 725s --------------- 725s PASSED 725s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 725s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '29' because it was < 2 characters long 725s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '57' because it was < 2 characters long 725s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 725s Warning: skipping read '58' because it was < 2 characters long 725s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '60' because it was < 2 characters long 725s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '74' because it was < 2 characters long 725s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 725s Warning: skipping read '88' because it was < 2 characters long 725s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '90' because it was < 2 characters long 725s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '95' because it was < 2 characters long 725s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '98' because it was < 2 characters long 725s Warning: skipping read '123' because length (1) <= # seed mismatches (0) 725s Warning: skipping read '123' because it was < 2 characters long 725s Warning: skipping read '157' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '157' because it was < 2 characters long 725s 168 reads; of these: 725s 168 (100.00%) were unpaired; of these: 725s 168 (100.00%) aligned 0 times 725s 0 (0.00%) aligned exactly 1 time 725s 0 (0.00%) aligned >1 times 725s 0.00% overall alignment rate 725s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 725s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 725s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 725s Flattened IUPAC characters 725s Mutating sequence Sim.pm.1 725s Introducing 23 SNPs, 2/1 ref/read gaps, and 0 rearrangements 725s Finished SNPs 725s Finished ref gaps 725s Finished read gaps 725s Mutating sequence Sim.pm.2 725s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 725s Finished SNPs 725s Finished ref gaps 725s Finished read gaps 725s Mutated reference genome to subject genome 725s SNPs introduced: 28 725s Reference gaps introduced: 2 725s Read gaps introduced: 1 725s Rearrangements introduced: 1 725s Created read sampler 725s Sampling 147 reads 725s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 725s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 725s parsing sequence Sim.pm.1... 725s parsing sequence Sim.pm.2... 725s Parsed 40 reference bases 725s *** Run 58 of 100 725s /usr/bin/bowtie2 --nofw --cp-ival 1 --local --norc --rdg 18.3742470721765 -k 13 --score-min L,5.43933616408313,3.14646030424588 --large-index --cp-min 4 --np 7 -r -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.raw -2 /tmp/Sim.pm.qtk7xXsv_2.raw 725s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 725s Warning: skipping mate #2 of read '2' because it was < 2 characters long 725s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 725s Warning: skipping mate #2 of read '44' because it was < 2 characters long 725s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (0) 725s Warning: skipping mate #2 of read '73' because it was < 2 characters long 725s Read 50 alignments... 725s Warning: skipping mate #1 of read '134' because length (1) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '134' because it was < 2 characters long 725s Read 100 alignments... 725s 147 reads; of these: 725s 147 (100.00%) were paired; of these: 725s 147 (100.00%) aligned concordantly 0 times 725s 0 (0.00%) aligned concordantly exactly 1 time 725s 0 (0.00%) aligned concordantly >1 times 725s ---- 725s 147 pairs aligned concordantly 0 times; of these: 725s 0 (0.00%) aligned discordantly 1 time 725s ---- 725s 147 pairs aligned 0 times concordantly or discordantly; of these: 725s 294 mates make up the pairs; of these: 725s 294 (100.00%) aligned 0 times 725s 0 (0.00%) aligned exactly 1 time 725s 0 (0.00%) aligned >1 times 725s 0.00% overall alignment rate 725s Read 150 alignments... 725s Read 200 alignments... 725s Read 250 alignments... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 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line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s /usr/bin/bowtie2 --nofw --cp-ival 1 --local --norc --rdg 18.3742470721765 -k 13 --score-min L,5.43933616408313,3.14646030424588 --large-index --cp-min 4 --np 7 -r -p 4 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.raw -2 /tmp/Sim.pm.qtk7xXsv_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s --- Summary --- 725s Read 1 reference strings 725s Checked 0 alignments, 0 edits 725s --------------- 725s PASSED 725s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 725s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 725s Warning: skipping mate #2 of read '2' because it was < 2 characters long 725s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 725s Warning: skipping mate #2 of read '44' because it was < 2 characters long 725s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (0) 725s Warning: skipping mate #2 of read '73' because it was < 2 characters long 725s Warning: skipping mate #1 of read '134' because length (1) <= # seed mismatches (0) 725s Warning: skipping mate #1 of read '134' because it was < 2 characters long 725s 147 reads; of these: 725s 147 (100.00%) were paired; of these: 725s 147 (100.00%) aligned concordantly 0 times 725s 0 (0.00%) aligned concordantly exactly 1 time 725s 0 (0.00%) aligned concordantly >1 times 725s ---- 725s 147 pairs aligned concordantly 0 times; of these: 725s 0 (0.00%) aligned discordantly 1 time 725s ---- 725s 147 pairs aligned 0 times concordantly or discordantly; of these: 725s 294 mates make up the pairs; of these: 725s 294 (100.00%) aligned 0 times 725s 0 (0.00%) aligned exactly 1 time 725s 0 (0.00%) aligned >1 times 725s 0.00% overall alignment rate 725s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 725s Flattened IUPAC characters 725s Mutating sequence Sim.pm.1 725s Introducing 2 SNPs, 3/0 ref/read gaps, and 1 rearrangements 725s Finished SNPs 725s Finished ref gaps 725s Finished read gaps 725s Mutating sequence Sim.pm.2 725s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 725s Finished SNPs 725s Finished ref gaps 725s Finished read gaps 725s *** Run 59 of 100 725s /usr/bin/bowtie2 --rfg 37.9439546136354,2.31159983085747 --trim5 6 --cp-ival 1 --ma 31.2181503612282 --score-min L,5.75477000845385,9.89775165697043 --mm --cp-min 2 --np 4 --large-index -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta 725s Mutated reference genome to subject genome 725s SNPs introduced: 11 725s Reference gaps introduced: 3 725s Read gaps introduced: 0 725s Rearrangements introduced: 1 725s Created read sampler 725s Sampling 65 reads 725s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 725s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 725s parsing sequence Sim.pm.1... 725s parsing sequence Sim.pm.2... 725s Parsed 40 reference bases 725s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 725s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 725s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '4' because it was < 2 characters long 725s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 725s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '17' because it was < 2 characters long 725s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 725s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '21' because it was < 2 characters long 725s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 725s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '23' because it was < 2 characters long 725s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 725s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '28' because it was < 2 characters long 725s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 725s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '29' because it was < 2 characters long 725s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 725s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '33' because it was < 2 characters long 725s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 725s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '41' because it was < 2 characters long 725s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 725s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '43' because it was < 2 characters long 725s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 725s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '51' because it was < 2 characters long 725s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 725s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 725s Warning: skipping read '54' because it was < 2 characters long 725s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 725s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 725s 65 reads; of these: 725s 65 (100.00%) were unpaired; of these: 725s 59 (90.77%) aligned 0 times 725s 4 (6.15%) aligned exactly 1 time 725s 2 (3.08%) aligned >1 times 725s 9.23% overall alignment rate 725s Read 50 alignments... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s ACATCTTCGCGAGGAGG 725s ACATCTTCGCGAGGAGG 725s Processing line... 725s Processing line... 725s GC 725s GC 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s GCCGGGGGCCTGCGC 725s GCCGGGGGCCTGCGC 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s CC 725s CC 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s GCCGGGGG 725s GCCGGGGG 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s Processing line... 725s TTCG 725s TTCG 725s Processing line... 725s --- Summary --- 725s Read 1 reference strings 725s Checked 6 alignments, 0 edits 725s --------------- 725s PASSED 725s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 725s /usr/bin/bowtie2 --rfg 37.9439546136354,2.31159983085747 --trim5 6 --cp-ival 1 --ma 31.2181503612282 --score-min L,5.75477000845385,9.89775165697043 --mm --cp-min 2 --np 4 --large-index -f -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 726s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 726s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 726s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '4' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 726s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '17' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 726s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '21' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 726s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '23' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 726s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '28' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 726s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '29' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 726s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '33' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 726s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '41' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 726s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '43' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 726s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '51' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 726s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '54' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 726s 65 reads; of these: 726s 65 (100.00%) were unpaired; of these: 726s 59 (90.77%) aligned 0 times 726s 4 (6.15%) aligned exactly 1 time 726s 2 (3.08%) aligned >1 times 726s 9.23% overall alignment rate 726s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 726s Flattened IUPAC characters 726s Mutating sequence Sim.pm.2 726s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 726s Finished SNPs 726s Finished ref gaps 726s Finished read gaps 726s Mutating sequence Sim.pm.1 726s Introducing 7 SNPs, 1/1 ref/read gaps, and 1 rearrangements 726s Finished SNPs 726s Finished ref gaps 726s Finished read gaps 726s Mutated reference genome to subject genome 726s SNPs introduced: 15 726s Reference gaps introduced: 1 726s Read gaps introduced: 1 726s Rearrangements introduced: 2 726s Created read sampler 726s Sampling 9 reads 726s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 726s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 726s parsing sequence Sim.pm.1... 726s parsing sequence Sim.pm.2... 726s Parsed 40 reference bases 726s *** Run 60 of 100 726s /usr/bin/bowtie2 --np 4 --cp-min 3 --large-index --mm --ma 27.4234478673865 --score-min L,6.61289089922594,4.80854852252017 -R 3 -k 3 -D 43 --cp-ival 2 --norc --trim3 7 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 726s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 726s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 726s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '4' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 726s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '5' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 726s 9 reads; of these: 726s 9 (100.00%) were unpaired; of these: 726s 7 (77.78%) aligned 0 times 726s 0 (0.00%) aligned exactly 1 time 726s 2 (22.22%) aligned >1 times 726s 22.22% overall alignment rate 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s TG 726s TG 726s Processing line... 726s TG 726s TG 726s /usr/bin/bowtie2 --np 4 --cp-min 3 --large-index --mm --ma 27.4234478673865 --score-min L,6.61289089922594,4.80854852252017 -R 3 -k 3 -D 43 --cp-ival 2 --norc --trim3 7 -r -p 3 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 726s Processing line... 726s CGA 726s CGA 726s Processing line... 726s CGA 726s CGA 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s --- Summary --- 726s Read 1 reference strings 726s Checked 4 alignments, 0 edits 726s --------------- 726s PASSED 726s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 726s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 726s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 726s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '4' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 726s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '5' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 726s 9 reads; of these: 726s 9 (100.00%) were unpaired; of these: 726s 7 (77.78%) aligned 0 times 726s 0 (0.00%) aligned exactly 1 time 726s 2 (22.22%) aligned >1 times 726s 22.22% overall alignment rate 726s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 726s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 726s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 726s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 726s /usr/bin/bowtie2 --np 4 --cp-min 3 --large-index --mm --ma 27.4234478673865 --score-min L,6.61289089922594,4.80854852252017 -R 3 -k 3 -D 43 --cp-ival 2 --norc --trim3 7 -r -p 4 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 726s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 726s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 726s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '4' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 726s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '5' because it was < 2 characters long 726s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 726s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 726s 9 reads; of these: 726s 9 (100.00%) were unpaired; of these: 726s 7 (77.78%) aligned 0 times 726s 0 (0.00%) aligned exactly 1 time 726s 2 (22.22%) aligned >1 times 726s 22.22% overall alignment rate 726s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 726s Flattened IUPAC characters 726s Mutating sequence Sim.pm.1 726s Introducing 8 SNPs, 2/1 ref/read gaps, and 0 rearrangements 726s Finished SNPs 726s Finished ref gaps 726s Finished read gaps 726s Mutating sequence Sim.pm.2 726s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 726s Finished SNPs 726s Finished ref gaps 726s Finished read gaps 726s Mutated reference genome to subject genome 726s SNPs introduced: 13 726s Reference gaps introduced: 2 726s Read gaps introduced: 1 726s Rearrangements introduced: 0 726s Created read sampler 726s Sampling 92 reads 726s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 726s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 726s *** Run 61 of 100 726s /usr/bin/bowtie2 --rfg 42.3360645899389 --trim3 5 --nofw --mp 8.75636554848918,7.75020203635431 --local --cp-ival 2 --mm --score-min L,6.56024051719366,1.47990579707175 -k 2 --cp-min 2 --large-index -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 726s parsing sequence Sim.pm.1... 726s parsing sequence Sim.pm.2... 726s Parsed 40 reference bases 726s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '6' because it was < 2 characters long 726s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '7' because it was < 2 characters long 726s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '9' because it was < 2 characters long 726s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '10' because it was < 2 characters long 726s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '14' because it was < 2 characters long 726s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '15' because it was < 2 characters long 726s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '30' because it was < 2 characters long 726s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '32' because it was < 2 characters long 726s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '38' because it was < 2 characters long 726s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '41' because it was < 2 characters long 726s Warning: skipping read '45' because length (1) <= # seed mismatches (0) 726s Warning: skipping read '45' because it was < 2 characters long 726s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '48' because it was < 2 characters long 726s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '53' because it was < 2 characters long 726s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '55' because it was < 2 characters long 726s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '73' because it was < 2 characters long 726s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 726s Warning: skipping read '88' because it was < 2 characters long 726s 92 reads; of these: 726s 92 (100.00%) were unpaired; of these: 726s 92 (100.00%) aligned 0 times 726s 0 (0.00%) aligned exactly 1 time 726s 0 (0.00%) aligned >1 times 726s 0.00% overall alignment rate 726s Read 50 alignments... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s Processing line... 726s --- Summary --- 726s Read 1 reference strings 726s Checked 0 alignments, 0 edits 726s --------------- 726s PASSED 726s Flattened IUPAC characters 726s Mutating sequence Sim.pm.2 726s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 726s Finished SNPs 726s Finished ref gaps 726s Finished read gaps 726s Mutating sequence Sim.pm.1 726s Introducing 8 SNPs, 1/0 ref/read gaps, and 1 rearrangements 726s Finished SNPs 726s Finished ref gaps 726s Finished read gaps 726s Mutated reference genome to subject genome 726s SNPs introduced: 11 726s Reference gaps introduced: 1 726s Read gaps introduced: 0 726s Rearrangements introduced: 1 726s Created read sampler 726s Sampling 165 reads 726s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 726s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 726s parsing sequence Sim.pm.1... 726s parsing sequence Sim.pm.2... 726s Parsed 40 reference bases 726s *** Run 62 of 100 726s /usr/bin/bowtie2 --trim5 1 --large-index --cp-min 2 --cp-ival 2 --local --score-min L,3.63928256851575,1.37666119356463 --mm --rfg 8.52140998715528 --rdg 47.4916989350666,4.97420891737927 --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq 727s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (1) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (1) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_150_150_1/1' because length (1) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_164_164_1/1' because length (1) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_164_164_1/1' because it was < 2 characters long 727s Read 50 alignments... 727s 165 reads; of these: 727s 165 (100.00%) were unpaired; of these: 727s 165 (100.00%) aligned 0 times 727s 0 (0.00%) aligned exactly 1 time 727s 0 (0.00%) aligned >1 times 727s 0.00% overall alignment rate 727s Read 100 alignments... 727s Read 150 alignments... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s /usr/bin/bowtie2 --trim5 1 --large-index --cp-min 2 --cp-ival 2 --local --score-min L,3.63928256851575,1.37666119356463 --mm --rfg 8.52140998715528 --rdg 47.4916989350666,4.97420891737927 --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s --- Summary --- 727s Read 1 reference strings 727s Checked 0 alignments, 0 edits 727s --------------- 727s PASSED 727s ALSO checking that bowtie2 and bowtie2-align match up 727s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (1) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (1) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_150_150_1/1' because length (1) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 727s Warning: skipping read 'R_1_1_1_164_164_1/1' because length (1) <= # seed mismatches (0) 727s Warning: skipping read 'R_1_1_1_164_164_1/1' because it was < 2 characters long 727s 165 reads; of these: 727s 165 (100.00%) were unpaired; of these: 727s 165 (100.00%) aligned 0 times 727s 0 (0.00%) aligned exactly 1 time 727s 0 (0.00%) aligned >1 times 727s 0.00% overall alignment rate 727s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 727s Flattened IUPAC characters 727s Mutating sequence Sim.pm.2 727s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 727s Finished SNPs 727s Finished ref gaps 727s Finished read gaps 727s Mutating sequence Sim.pm.1 727s Introducing 14 SNPs, 0/0 ref/read gaps, and 1 rearrangements 727s Finished SNPs 727s Finished ref gaps 727s Finished read gaps 727s Mutated reference genome to subject genome 727s SNPs introduced: 17 727s Reference gaps introduced: 0 727s Read gaps introduced: 0 727s Rearrangements introduced: 1 727s Created read sampler 727s Sampling 26 reads 727s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 727s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 727s parsing sequence Sim.pm.1... 727s parsing sequence Sim.pm.2... 727s Parsed 40 reference bases 727s *** Run 63 of 100 727s /usr/bin/bowtie2 --large-index --cp-min 3 --mm -D 15 --score-min L,5.22579223578439,5.60975046727284 --cp-ival 2 --local --norc -M 2 --rfg 45.3587781179213,5.8048079323064 -i S,1.93152685751197 --mp 9.14268861251349,6.50340935904058 -N 1 -L28 -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta 727s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 727s Warning: skipping read '5' because length (1) <= # seed mismatches (1) 727s Warning: skipping read '5' because it was < 2 characters long 727s 26 reads; of these: 727s 26 (100.00%) were unpaired; of these: 727s 26 (100.00%) aligned 0 times 727s 0 (0.00%) aligned exactly 1 time 727s 0 (0.00%) aligned >1 times 727s 0.00% overall alignment rate 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s /usr/bin/bowtie2 --large-index --cp-min 3 --mm -D 15 --score-min L,5.22579223578439,5.60975046727284 --cp-ival 2 --local --norc -M 2 --rfg 45.3587781179213,5.8048079323064 -i S,1.93152685751197 --mp 9.14268861251349,6.50340935904058 -N 1 -L28 -f -p 4 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s --- Summary --- 727s Read 1 reference strings 727s Checked 0 alignments, 0 edits 727s --------------- 727s PASSED 727s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 727s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 727s Warning: skipping read '5' because length (1) <= # seed mismatches (1) 727s Warning: skipping read '5' because it was < 2 characters long 727s 26 reads; of these: 727s 26 (100.00%) were unpaired; of these: 727s 26 (100.00%) aligned 0 times 727s 0 (0.00%) aligned exactly 1 time 727s 0 (0.00%) aligned >1 times 727s 0.00% overall alignment rate 727s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 727s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 727s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 727s Flattened IUPAC characters 727s Mutating sequence Sim.pm.1 727s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 727s Finished SNPs 727s Finished ref gaps 727s Finished read gaps 727s Mutating sequence Sim.pm.2 727s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 727s Finished SNPs 727s Finished ref gaps 727s Finished read gaps 727s Mutated reference genome to subject genome 727s SNPs introduced: 10 727s Reference gaps introduced: 0 727s Read gaps introduced: 1 727s Rearrangements introduced: 1 727s Created read sampler 727s Sampling 95 reads 727s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 727s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 727s parsing sequence Sim.pm.1... 727s parsing sequence Sim.pm.2... 727s *** Run 64 of 100 727s /usr/bin/bowtie2 --rfg 18.6124893371303,5.21382008314818 --trim3 3 -N 0 -L18 --mp 4.77721607036114,2.04157618690933 --local --cp-ival 1 --trim5 5 --n-ceil 0.90884894749716,0.857037068739604 --mm --score-min L,6.85382718573106,4.1327950238658 --cp-min 2 --np 2 --large-index -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 727s Parsed 40 reference bases 727s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '3' because it was < 2 characters long 727s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '5' because it was < 2 characters long 727s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '10' because it was < 2 characters long 727s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '11' because it was < 2 characters long 727s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '14' because it was < 2 characters long 727s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '23' because it was < 2 characters long 727s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '30' because it was < 2 characters long 727s Warning: skipping mate #1 of read '33' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '33' because it was < 2 characters long 727s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 727s Warning: skipping read '39' because it was < 2 characters long 727s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '42' because it was < 2 characters long 727s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '43' because it was < 2 characters long 727s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #2 of read '46' because it was < 2 characters long 727s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '50' because it was < 2 characters long 727s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '51' because it was < 2 characters long 727s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '52' because it was < 2 characters long 727s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 727s Warning: skipping read '53' because it was < 2 characters long 727s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '58' because it was < 2 characters long 727s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '62' because it was < 2 characters long 727s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 727s Warning: skipping read '69' because it was < 2 characters long 727s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '73' because it was < 2 characters long 727s Read 50 alignments... 727s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 727s Warning: skipping read '88' because it was < 2 characters long 727s Warning: skipping mate #1 of read '95' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '95' because it was < 2 characters long 727s Read 100 alignments... 727s 95 reads; of these: 727s 81 (85.26%) were paired; of these: 727s 81 (100.00%) aligned concordantly 0 times 727s 0 (0.00%) aligned concordantly exactly 1 time 727s 0 (0.00%) aligned concordantly >1 times 727s ---- 727s 81 pairs aligned concordantly 0 times; of these: 727s 0 (0.00%) aligned discordantly 1 time 727s ---- 727s 81 pairs aligned 0 times concordantly or discordantly; of these: 727s 162 mates make up the pairs; of these: 727s 162 (100.00%) aligned 0 times 727s 0 (0.00%) aligned exactly 1 time 727s 0 (0.00%) aligned >1 times 727s 14 (14.74%) were unpaired; of these: 727s 14 (100.00%) aligned 0 times 727s 0 (0.00%) aligned exactly 1 time 727s 0 (0.00%) aligned >1 times 727s 0.00% overall alignment rate 727s Read 150 alignments... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s Processing line... 727s /usr/bin/bowtie2 --rfg 18.6124893371303,5.21382008314818 --trim3 3 -N 0 -L18 --mp 4.77721607036114,2.04157618690933 --local --cp-ival 1 --trim5 5 --n-ceil 0.90884894749716,0.857037068739604 --mm --score-min L,6.85382718573106,4.1327950238658 --cp-min 2 --np 2 --large-index -f -p 2 -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 727s --- Summary --- 727s Read 1 reference strings 727s Checked 0 alignments, 0 edits 727s --------------- 727s PASSED 727s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 727s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '3' because it was < 2 characters long 727s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '5' because it was < 2 characters long 727s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '10' because it was < 2 characters long 727s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '11' because it was < 2 characters long 727s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '14' because it was < 2 characters long 727s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '23' because it was < 2 characters long 727s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '30' because it was < 2 characters long 727s Warning: skipping mate #1 of read '33' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '33' because it was < 2 characters long 727s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 727s Warning: skipping read '39' because it was < 2 characters long 727s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '42' because it was < 2 characters long 727s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '43' because it was < 2 characters long 727s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #2 of read '46' because it was < 2 characters long 727s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '50' because it was < 2 characters long 727s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '51' because it was < 2 characters long 727s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '52' because it was < 2 characters long 727s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 727s Warning: skipping read '53' because it was < 2 characters long 727s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '58' because it was < 2 characters long 727s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '62' because it was < 2 characters long 727s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 727s Warning: skipping read '69' because it was < 2 characters long 727s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '73' because it was < 2 characters long 727s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 727s Warning: skipping read '88' because it was < 2 characters long 727s Warning: skipping mate #1 of read '95' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '95' because it was < 2 characters long 727s 95 reads; of these: 727s 81 (85.26%) were paired; of these: 727s 81 (100.00%) aligned concordantly 0 times 727s 0 (0.00%) aligned concordantly exactly 1 time 727s 0 (0.00%) aligned concordantly >1 times 727s ---- 727s 81 pairs aligned concordantly 0 times; of these: 727s 0 (0.00%) aligned discordantly 1 time 727s ---- 727s 81 pairs aligned 0 times concordantly or discordantly; of these: 727s 162 mates make up the pairs; of these: 727s 162 (100.00%) aligned 0 times 727s 0 (0.00%) aligned exactly 1 time 727s 0 (0.00%) aligned >1 times 727s 14 (14.74%) were unpaired; of these: 727s 14 (100.00%) aligned 0 times 727s 0 (0.00%) aligned exactly 1 time 727s 0 (0.00%) aligned >1 times 727s 0.00% overall alignment rate 727s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 727s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 727s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 727s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 727s /usr/bin/bowtie2 --rfg 18.6124893371303,5.21382008314818 --trim3 3 -N 0 -L18 --mp 4.77721607036114,2.04157618690933 --local --cp-ival 1 --trim5 5 --n-ceil 0.90884894749716,0.857037068739604 --mm --score-min L,6.85382718573106,4.1327950238658 --cp-min 2 --np 2 --large-index -f -p 3 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 727s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '3' because it was < 2 characters long 727s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '5' because it was < 2 characters long 727s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '10' because it was < 2 characters long 727s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '11' because it was < 2 characters long 727s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '14' because it was < 2 characters long 727s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '23' because it was < 2 characters long 727s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '30' because it was < 2 characters long 727s Warning: skipping mate #1 of read '33' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '33' because it was < 2 characters long 727s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 727s Warning: skipping read '39' because it was < 2 characters long 727s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '42' because it was < 2 characters long 727s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '43' because it was < 2 characters long 727s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #2 of read '46' because it was < 2 characters long 727s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '50' because it was < 2 characters long 727s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '51' because it was < 2 characters long 727s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '52' because it was < 2 characters long 727s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 727s Warning: skipping read '53' because it was < 2 characters long 727s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '58' because it was < 2 characters long 727s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '62' because it was < 2 characters long 727s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 727s Warning: skipping read '69' because it was < 2 characters long 727s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '73' because it was < 2 characters long 727s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 727s Warning: skipping read '88' because it was < 2 characters long 727s Warning: skipping mate #1 of read '95' because length (1) <= # seed mismatches (0) 727s Warning: skipping mate #1 of read '95' because it was < 2 characters long 727s 95 reads; of these: 727s 81 (85.26%) were paired; of these: 727s 81 (100.00%) aligned concordantly 0 times 727s 0 (0.00%) aligned concordantly exactly 1 time 727s 0 (0.00%) aligned concordantly >1 times 727s ---- 727s 81 pairs aligned concordantly 0 times; of these: 727s 0 (0.00%) aligned discordantly 1 time 727s ---- 727s 81 pairs aligned 0 times concordantly or discordantly; of these: 727s 162 mates make up the pairs; of these: 727s 162 (100.00%) aligned 0 times 727s 0 (0.00%) aligned exactly 1 time 727s 0 (0.00%) aligned >1 times 727s 14 (14.74%) were unpaired; of these: 727s 14 (100.00%) aligned 0 times 727s 0 (0.00%) aligned exactly 1 time 727s 0 (0.00%) aligned >1 times 727s 0.00% overall alignment rate 727s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 727s Flattened IUPAC characters 727s Mutating sequence Sim.pm.2 727s Introducing 1 SNPs, 2/0 ref/read gaps, and 0 rearrangements 727s Finished SNPs 727s Finished ref gaps 727s Finished read gaps 727s Mutating sequence Sim.pm.1 727s Introducing 14 SNPs, 0/0 ref/read gaps, and 2 rearrangements 727s Finished SNPs 727s Finished ref gaps 727s Finished read gaps 727s Mutated reference genome to subject genome 727s SNPs introduced: 15 727s Reference gaps introduced: 2 727s Read gaps introduced: 0 727s Rearrangements introduced: 2 727s Created read sampler 727s Sampling 118 reads 727s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 727s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 727s parsing sequence Sim.pm.1... 727s parsing sequence Sim.pm.2... 727s Parsed 40 reference bases 727s *** Run 65 of 100 727s /usr/bin/bowtie2 --score-min L,2.70510457453033,5.1959718580626 --ma 34.8774008502155 -k 3 -R 2 -i L,0.45944799787974 --large-index --cp-min 3 --np 1 --trim5 8 --cp-ival 2 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 728s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 728s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 728s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '4' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 728s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '11' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 728s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '14' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 728s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '15' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 728s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '26' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 728s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '33' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 728s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '34' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 728s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '42' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 728s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '48' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 728s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '49' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 728s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '50' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 728s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 728s Warning: skipping read '57' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 728s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '59' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 728s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '63' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 728s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '68' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 728s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '69' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 728s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '71' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 728s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '72' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 728s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '86' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 728s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '88' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 728s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '91' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 728s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '95' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 728s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '98' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 728s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 728s Warning: skipping read '99' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 728s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '100' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 728s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '102' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 728s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '103' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 728s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '106' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 728s 118 reads; of these: 728s 118 (100.00%) were unpaired; of these: 728s 108 (91.53%) aligned 0 times 728s 3 (2.54%) aligned exactly 1 time 728s 7 (5.93%) aligned >1 times 728s 8.47% overall alignment rate 728s Read 50 alignments... 728s Read 100 alignments... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s CCG 728s CCG 728s Processing line... 728s CGG 728s CGG 728s Processing line... 728s CGG 728s CGG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s CG 728s CG 728s Processing line... 728s CG 728s CG 728s Processing line... 728s CG 728s CG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s CGA 728s CGA 728s Processing line... 728s CGA 728s CGA 728s Processing line... 728s TCG 728s TCG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s /usr/bin/bowtie2 --score-min L,2.70510457453033,5.1959718580626 --ma 34.8774008502155 -k 3 -R 2 -i L,0.45944799787974 --large-index --cp-min 3 --np 1 --trim5 8 --cp-ival 2 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s ACATCTTCGCGA 728s ACATCTTCGCGA 728s Processing line... 728s GGGG 728s GGGG 728s Processing line... 728s GGGG 728s GGGG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s CCGGGGG 728s CCGGGGG 728s Processing line... 728s GCGCGACG 728s GCGCGACG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s GG 728s GG 728s Processing line... 728s GG 728s GG 728s Processing line... 728s GG 728s GG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s AGG 728s AGG 728s Processing line... 728s AGG 728s AGG 728s Processing line... 728s CCT 728s CCT 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s CA 728s CA 728s Processing line... 728s TG 728s TG 728s Processing line... 728s TG 728s TG 728s Processing line... 728s Processing line... 728s Processing line... 728s --- Summary --- 728s Read 1 reference strings 728s Checked 23 alignments, 0 edits 728s --------------- 728s PASSED 728s ALSO checking that bowtie2 and bowtie2-align match up 728s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 728s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 728s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '4' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 728s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '11' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 728s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '14' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 728s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '15' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 728s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '26' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 728s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '33' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 728s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '34' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 728s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '42' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 728s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '48' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 728s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '49' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 728s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '50' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 728s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 728s Warning: skipping read '57' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 728s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '59' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 728s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '63' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 728s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '68' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 728s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '69' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 728s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '71' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 728s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '72' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 728s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '86' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 728s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '88' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 728s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '91' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 728s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '95' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 728s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '98' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 728s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 728s Warning: skipping read '99' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 728s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '100' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 728s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '102' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 728s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '103' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 728s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '106' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 728s 118 reads; of these: 728s 118 (100.00%) were unpaired; of these: 728s 108 (91.53%) aligned 0 times 728s 3 (2.54%) aligned exactly 1 time 728s 7 (5.93%) aligned >1 times 728s 8.47% overall alignment rate 728s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 728s Flattened IUPAC characters 728s Mutating sequence Sim.pm.1 728s Introducing 5 SNPs, 0/1 ref/read gaps, and 1 rearrangements 728s Finished SNPs 728s Finished ref gaps 728s Finished read gaps 728s Mutating sequence Sim.pm.2 728s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 728s Finished SNPs 728s Finished ref gaps 728s Finished read gaps 728s Mutated reference genome to subject genome 728s SNPs introduced: 7 728s Reference gaps introduced: 1 728s Read gaps introduced: 1 728s Rearrangements introduced: 1 728s Created read sampler 728s Sampling 123 reads 728s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 728s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 728s parsing sequence Sim.pm.1... 728s *** Run 66 of 100 728s /usr/bin/bowtie2 --large-index --cp-min 3 --cp-ival 1 -D 33 -i L,0.146976441607344,0.292872876345271 -N 1 -L29 --score-min L,9.75565809161912,6.72308237406519 --rfg 32.472708156882 --rdg 7.03849909886365 --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq 728s parsing sequence Sim.pm.2... 728s Parsed 40 reference bases 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 728s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (1) 728s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 728s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (1) 728s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 728s Read 50 alignments... 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 728s Read 100 alignments... 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 728s Read 150 alignments... 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 728s Warning: skipping mate #2 of read 'R_1_1_1_110_110_1/1' because length (1) <= # seed mismatches (1) 728s Warning: skipping mate #2 of read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 728s 123 reads; of these: 728s 123 (100.00%) were paired; of these: 728s 122 (99.19%) aligned concordantly 0 times 728s 0 (0.00%) aligned concordantly exactly 1 time 728s 1 (0.81%) aligned concordantly >1 times 728s ---- 728s 122 pairs aligned concordantly 0 times; of these: 728s 0 (0.00%) aligned discordantly 1 time 728s ---- 728s 122 pairs aligned 0 times concordantly or discordantly; of these: 728s 244 mates make up the pairs; of these: 728s 228 (93.44%) aligned 0 times 728s 7 (2.87%) aligned exactly 1 time 728s 9 (3.69%) aligned >1 times 728s 7.32% overall alignment rate 728s Read 200 alignments... 728s Read 250 alignments... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s AGG 728s AGG 728s Processing line... 728s Processing line... 728s GC 728s GC 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s AC 728s AC 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s CGCGAGG 728s CGCGAGG 728s Processing line... 728s Processing line... 728s TCGC 728s TCGC 728s Processing line... 728s Processing line... 728s CGCGAGGAGGA 728s CGCGAGGAGGA 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s TG 728s TG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s TT 728s TT 728s Processing line... 728s Processing line... 728s GCGAGGAG 728s GCGAGGAG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s GA 728s GA 728s Processing line... 728s AT 728s AT 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s TTC 728s TTC 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s GG 728s GG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s GCGAGGAGG 728s GCGAGGAGG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s AC 728s AC 728s Processing line... 728s GGAG 728s GGAG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s AC 728s AC 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s ACAT 728s ACAT 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s --- Summary --- 728s Read 1 reference strings 728s Checked 18 alignments, 0 edits 728s --------------- 728s PASSED 728s ALSO checking that bowtie2 and bowtie2-align match up 728s /usr/bin/bowtie2 --large-index --cp-min 3 --cp-ival 1 -D 33 -i L,0.146976441607344,0.292872876345271 -N 1 -L29 --score-min L,9.75565809161912,6.72308237406519 --rfg 32.472708156882 --rdg 7.03849909886365 --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 728s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (1) 728s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 728s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (1) 728s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 728s Warning: skipping mate #2 of read 'R_1_1_1_110_110_1/1' because length (1) <= # seed mismatches (1) 728s Warning: skipping mate #2 of read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 728s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 728s 123 reads; of these: 728s 123 (100.00%) were paired; of these: 728s 122 (99.19%) aligned concordantly 0 times 728s 0 (0.00%) aligned concordantly exactly 1 time 728s 1 (0.81%) aligned concordantly >1 times 728s ---- 728s 122 pairs aligned concordantly 0 times; of these: 728s 0 (0.00%) aligned discordantly 1 time 728s ---- 728s 122 pairs aligned 0 times concordantly or discordantly; of these: 728s 244 mates make up the pairs; of these: 728s 228 (93.44%) aligned 0 times 728s 7 (2.87%) aligned exactly 1 time 728s 9 (3.69%) aligned >1 times 728s 7.32% overall alignment rate 728s Flattened IUPAC characters 728s Mutating sequence Sim.pm.1 728s Introducing 17 SNPs, 0/1 ref/read gaps, and 0 rearrangements 728s Finished SNPs 728s Finished ref gaps 728s Finished read gaps 728s Mutating sequence Sim.pm.2 728s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 728s Finished SNPs 728s Finished ref gaps 728s Finished read gaps 728s Mutated reference genome to subject genome 728s SNPs introduced: 22 728s Reference gaps introduced: 1 728s Read gaps introduced: 1 728s Rearrangements introduced: 0 728s Created read sampler 728s Sampling 72 reads 728s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 728s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 728s *** Run 67 of 100 728s /usr/bin/bowtie2 --n-ceil 0.242961144843929,0.409649100303731 --trim5 5 -M 3 --large-index --cp-min 2 --cp-ival 4 -D 45 --mp 6.9769458398411,1.74358678944636 --score-min L,5.29915410858956,7.05845726978447 --nofw --mm -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta 728s parsing sequence Sim.pm.1... 728s parsing sequence Sim.pm.2... 728s Parsed 40 reference bases 728s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 728s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 728s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '4' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 728s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '6' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 728s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '10' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 728s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '14' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 728s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '16' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 728s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '39' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 728s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 728s Warning: skipping read '44' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 728s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '46' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 728s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '52' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 728s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '55' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 728s 72 reads; of these: 728s 72 (100.00%) were unpaired; of these: 728s 67 (93.06%) aligned 0 times 728s 3 (4.17%) aligned exactly 1 time 728s 2 (2.78%) aligned >1 times 728s 6.94% overall alignment rate 728s Read 50 alignments... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s GGG 728s GGG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s /usr/bin/bowtie2 --n-ceil 0.242961144843929,0.409649100303731 --trim5 5 -M 3 --large-index --cp-min 2 --cp-ival 4 -D 45 --mp 6.9769458398411,1.74358678944636 --score-min L,5.29915410858956,7.05845726978447 --nofw --mm -f -p 4 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s CA 728s CA 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s CATC 728s CATC 728s Processing line... 728s GCGAGG 728s GCGAGG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s GCG 728s GCG 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s Processing line... 728s --- Summary --- 728s Read 1 reference strings 728s Checked 5 alignments, 0 edits 728s --------------- 728s PASSED 728s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 728s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 728s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 728s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '4' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 728s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '6' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 728s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '10' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 728s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '14' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 728s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '16' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 728s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '39' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 728s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 728s Warning: skipping read '44' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 728s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '46' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 728s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '52' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 728s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 728s Warning: skipping read '55' because it was < 2 characters long 728s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 728s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 728s 72 reads; of these: 728s 72 (100.00%) were unpaired; of these: 728s 67 (93.06%) aligned 0 times 728s 3 (4.17%) aligned exactly 1 time 728s 2 (2.78%) aligned >1 times 728s 6.94% overall alignment rate 728s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 728s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 728s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 728s Flattened IUPAC characters 728s Mutating sequence Sim.pm.1 728s Introducing 0 SNPs, 0/2 ref/read gaps, and 4 rearrangements 728s Finished SNPs 728s Finished ref gaps 728s Finished read gaps 728s Mutating sequence Sim.pm.2 728s Introducing 3 SNPs, 0/2 ref/read gaps, and 0 rearrangements 728s Finished SNPs 728s Finished ref gaps 728s Finished read gaps 728s Mutated reference genome to subject genome 728s SNPs introduced: 3 728s Reference gaps introduced: 0 728s Read gaps introduced: 4 728s Rearrangements introduced: 4 728s Created read sampler 728s Sampling 20 reads 728s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 728s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 728s parsing sequence Sim.pm.1... 728s parsing sequence Sim.pm.2... 728s Parsed 40 reference bases 728s *** Run 68 of 100 728s /usr/bin/bowtie2 --large-index --cp-min 7 --np 3 --rdg 8.59586723784391,10.9062832859503 --score-min L,9.55681145392776,7.27157543510381 --cp-ival 1 --local --norc --rfg 47.5878015965983,3.14050879280234 -N 1 -L13 --nofw -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta 729s 20 reads; of these: 729s 20 (100.00%) were unpaired; of these: 729s 20 (100.00%) aligned 0 times 729s 0 (0.00%) aligned exactly 1 time 729s 0 (0.00%) aligned >1 times 729s 0.00% overall alignment rate 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s --- Summary --- 729s Read 1 reference strings 729s Checked 0 alignments, 0 edits 729s --------------- 729s PASSED 729s Flattened IUPAC characters 729s Mutating sequence Sim.pm.1 729s Introducing 2 SNPs, 0/2 ref/read gaps, and 0 rearrangements 729s Finished SNPs 729s Finished ref gaps 729s Finished read gaps 729s Mutating sequence Sim.pm.2 729s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 729s Finished SNPs 729s Finished ref gaps 729s Finished read gaps 729s Mutated reference genome to subject genome 729s SNPs introduced: 4 729s Reference gaps introduced: 1 729s Read gaps introduced: 2 729s Rearrangements introduced: 0 729s Created read sampler 729s Sampling 135 reads 729s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 729s *** Run 69 of 100 729s /usr/bin/bowtie2 --score-min L,9.18074798647481,1.98670991457549 --mp 6.55592356447759,2.19015023352707 --rdg 5.17325036587486,3.25746219506687 --rfg 15.9553054641937 --mm --large-index -a --cp-min 3 --trim5 9 --local --cp-ival 1 --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq 729s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 729s parsing sequence Sim.pm.1... 729s parsing sequence Sim.pm.2... 729s Parsed 40 reference bases 729s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (1) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (1) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 729s 135 reads; of these: 729s 135 (100.00%) were unpaired; of these: 729s 135 (100.00%) aligned 0 times 729s 0 (0.00%) aligned exactly 1 time 729s 0 (0.00%) aligned >1 times 729s 0.00% overall alignment rate 729s Read 50 alignments... 729s Read 100 alignments... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s --- Summary --- 729s /usr/bin/bowtie2 --score-min L,9.18074798647481,1.98670991457549 --mp 6.55592356447759,2.19015023352707 --rdg 5.17325036587486,3.25746219506687 --rfg 15.9553054641937 --mm --large-index -a --cp-min 3 --trim5 9 --local --cp-ival 1 --qseq -p 3 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 729s Read 1 reference strings 729s Checked 0 alignments, 0 edits 729s --------------- 729s PASSED 729s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 729s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (1) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (1) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 729s 135 reads; of these: 729s 135 (100.00%) were unpaired; of these: 729s 135 (100.00%) aligned 0 times 729s 0 (0.00%) aligned exactly 1 time 729s 0 (0.00%) aligned >1 times 729s 0.00% overall alignment rate 729s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 729s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 729s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 729s /usr/bin/bowtie2 --score-min L,9.18074798647481,1.98670991457549 --mp 6.55592356447759,2.19015023352707 --rdg 5.17325036587486,3.25746219506687 --rfg 15.9553054641937 --mm --large-index -a --cp-min 3 --trim5 9 --local --cp-ival 1 --qseq -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 729s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 729s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (1) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_99_99_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_99_99_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (1) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 729s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 729s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 729s 135 reads; of these: 729s 135 (100.00%) were unpaired; of these: 729s 135 (100.00%) aligned 0 times 729s 0 (0.00%) aligned exactly 1 time 729s 0 (0.00%) aligned >1 times 729s 0.00% overall alignment rate 729s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 729s Flattened IUPAC characters 729s Mutating sequence Sim.pm.2 729s Introducing 7 SNPs, 2/0 ref/read gaps, and 0 rearrangements 729s Finished SNPs 729s Finished ref gaps 729s Finished read gaps 729s Mutating sequence Sim.pm.1 729s Introducing 11 SNPs, 0/1 ref/read gaps, and 1 rearrangements 729s Finished SNPs 729s Finished ref gaps 729s Finished read gaps 729s Mutated reference genome to subject genome 729s SNPs introduced: 18 729s Reference gaps introduced: 2 729s Read gaps introduced: 1 729s Rearrangements introduced: 1 729s Created read sampler 729s Sampling 10 reads 729s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 729s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 729s *** Run 70 of 100 729s /usr/bin/bowtie2 --score-min L,2.84341199215968,1.61432189504493 -D 23 -R 4 --large-index --cp-min 5 --np 1 --trim3 4 --mp 3.6261227159856,3.38858058072131 --local --cp-ival 1 -a -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq 729s parsing sequence Sim.pm.1... 729s parsing sequence Sim.pm.2... 729s Parsed 40 reference bases 729s 10 reads; of these: 729s 10 (100.00%) were paired; of these: 729s 10 (100.00%) aligned concordantly 0 times 729s 0 (0.00%) aligned concordantly exactly 1 time 729s 0 (0.00%) aligned concordantly >1 times 729s ---- 729s 10 pairs aligned concordantly 0 times; of these: 729s 0 (0.00%) aligned discordantly 1 time 729s ---- 729s 10 pairs aligned 0 times concordantly or discordantly; of these: 729s 20 mates make up the pairs; of these: 729s 20 (100.00%) aligned 0 times 729s 0 (0.00%) aligned exactly 1 time 729s 0 (0.00%) aligned >1 times 729s 0.00% overall alignment rate 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s /usr/bin/bowtie2 --score-min L,2.84341199215968,1.61432189504493 -D 23 -R 4 --large-index --cp-min 5 --np 1 --trim3 4 --mp 3.6261227159856,3.38858058072131 --local --cp-ival 1 -a -q -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s --- Summary --- 729s Read 1 reference strings 729s Checked 0 alignments, 0 edits 729s --------------- 729s PASSED 729s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 729s 10 reads; of these: 729s 10 (100.00%) were paired; of these: 729s 10 (100.00%) aligned concordantly 0 times 729s 0 (0.00%) aligned concordantly exactly 1 time 729s 0 (0.00%) aligned concordantly >1 times 729s ---- 729s 10 pairs aligned concordantly 0 times; of these: 729s 0 (0.00%) aligned discordantly 1 time 729s ---- 729s 10 pairs aligned 0 times concordantly or discordantly; of these: 729s 20 mates make up the pairs; of these: 729s 20 (100.00%) aligned 0 times 729s 0 (0.00%) aligned exactly 1 time 729s 0 (0.00%) aligned >1 times 729s 0.00% overall alignment rate 729s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 729s Flattened IUPAC characters 729s Mutating sequence Sim.pm.1 729s Introducing 14 SNPs, 0/0 ref/read gaps, and 0 rearrangements 729s Finished SNPs 729s Finished ref gaps 729s Finished read gaps 729s Mutating sequence Sim.pm.2 729s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 729s Finished SNPs 729s Finished ref gaps 729s Finished read gaps 729s Mutated reference genome to subject genome 729s SNPs introduced: 16 729s Reference gaps introduced: 0 729s Read gaps introduced: 1 729s Rearrangements introduced: 1 729s Created read sampler 729s Sampling 54 reads 729s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 729s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 729s parsing sequence Sim.pm.1... 729s parsing sequence Sim.pm.2... 729s Parsed 40 reference bases 729s *** Run 71 of 100 729s /usr/bin/bowtie2 --mm --rdg 45.4121841686013,7.11995944995273 --gbar 1 -R 4 --score-min L,5.53363197918922,3.37871541557406 --ma 23.3931696230636 --trim3 8 --cp-ival 2 --trim5 3 -a --large-index --cp-min 2 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 729s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 729s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 729s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '7' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 729s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '8' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 729s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '9' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 729s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '12' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 729s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '15' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 729s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '17' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 729s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '19' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 729s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '22' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 729s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '23' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 729s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '25' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 729s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '26' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 729s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '27' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 729s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '30' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 729s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '34' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 729s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '37' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 729s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '40' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 729s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '41' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 729s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '46' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 729s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '47' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 729s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '49' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 729s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '50' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 729s 54 reads; of these: 729s 54 (100.00%) were unpaired; of these: 729s 49 (90.74%) aligned 0 times 729s 0 (0.00%) aligned exactly 1 time 729s 5 (9.26%) aligned >1 times 729s 9.26% overall alignment rate 729s Read 50 alignments... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s TC 729s TC 729s Processing line... 729s GA 729s GA 729s Processing line... 729s GA 729s GA 729s Processing line... 729s GA 729s GA 729s Processing line... 729s TC 729s TC 729s Processing line... 729s GA 729s GA 729s Processing line... 729s Processing line... 729s CA 729s CA 729s Processing line... 729s TG 729s TG 729s Processing line... 729s TG 729s TG 729s Processing line... 729s Processing line... 729s Processing line... 729s AC 729s AC 729s Processing line... 729s AC 729s AC 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s CGC 729s CGC 729s Processing line... 729s GCG 729s GCG 729s Processing line... 729s GCG 729s GCG 729s Processing line... 729s CGC 729s CGC 729s Processing line... 729s GCG 729s GCG 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s TG 729s TG 729s Processing line... 729s CA 729s CA 729s Processing line... 729s TG 729s TG 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s Processing line... 729s --- Summary --- 729s Read 1 reference strings 729s Checked 19 alignments, 0 edits 729s --------------- 729s PASSED 729s ALSO checking that bowtie2 and bowtie2-align match up 729s /usr/bin/bowtie2 --mm --rdg 45.4121841686013,7.11995944995273 --gbar 1 -R 4 --score-min L,5.53363197918922,3.37871541557406 --ma 23.3931696230636 --trim3 8 --cp-ival 2 --trim5 3 -a --large-index --cp-min 2 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 729s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 729s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 729s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 729s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '7' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 729s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '8' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 729s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 729s Warning: skipping read '9' because it was < 2 characters long 729s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 730s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '12' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 730s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '15' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 730s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '17' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 730s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '19' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 730s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '22' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 730s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '23' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 730s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '25' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 730s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '26' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 730s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '27' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 730s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '30' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 730s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '34' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 730s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '37' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 730s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '40' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 730s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '41' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 730s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '46' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 730s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '47' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 730s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '49' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 730s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '50' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 730s 54 reads; of these: 730s 54 (100.00%) were unpaired; of these: 730s 49 (90.74%) aligned 0 times 730s 0 (0.00%) aligned exactly 1 time 730s 5 (9.26%) aligned >1 times 730s 9.26% overall alignment rate 730s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 730s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 730s /usr/bin/bowtie2 --mm --rdg 45.4121841686013,7.11995944995273 --gbar 1 -R 4 --score-min L,5.53363197918922,3.37871541557406 --ma 23.3931696230636 --trim3 8 --cp-ival 2 --trim5 3 -a --large-index --cp-min 2 -r -p 2 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 730s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 730s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 730s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '7' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 730s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '8' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 730s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '9' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 730s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '12' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 730s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '15' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 730s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '17' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 730s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '19' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 730s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '22' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 730s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '23' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 730s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '25' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 730s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '26' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 730s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '27' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 730s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '30' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 730s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '34' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 730s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '37' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 730s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '40' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 730s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '41' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 730s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '46' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 730s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '47' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 730s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '49' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 730s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '50' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 730s 54 reads; of these: 730s 54 (100.00%) were unpaired; of these: 730s 49 (90.74%) aligned 0 times 730s 0 (0.00%) aligned exactly 1 time 730s 5 (9.26%) aligned >1 times 730s 9.26% overall alignment rate 730s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 730s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 730s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 730s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 730s /usr/bin/bowtie2 --mm --rdg 45.4121841686013,7.11995944995273 --gbar 1 -R 4 --score-min L,5.53363197918922,3.37871541557406 --ma 23.3931696230636 --trim3 8 --cp-ival 2 --trim5 3 -a --large-index --cp-min 2 -r -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 730s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 730s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 730s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '7' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 730s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '8' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 730s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '9' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 730s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '12' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 730s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '15' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 730s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '17' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 730s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '19' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 730s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '22' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 730s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '23' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 730s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '25' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 730s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '26' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 730s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '27' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 730s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '30' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 730s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '34' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 730s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '37' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 730s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '40' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 730s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '41' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 730s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '46' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 730s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '47' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 730s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '49' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 730s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '50' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 730s 54 reads; of these: 730s 54 (100.00%) were unpaired; of these: 730s 49 (90.74%) aligned 0 times 730s 0 (0.00%) aligned exactly 1 time 730s 5 (9.26%) aligned >1 times 730s 9.26% overall alignment rate 730s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 730s Flattened IUPAC characters 730s Mutating sequence Sim.pm.1 730s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 730s Finished SNPs 730s Finished ref gaps 730s Finished read gaps 730s Mutating sequence Sim.pm.2 730s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 730s Finished SNPs 730s Finished ref gaps 730s Finished read gaps 730s Mutated reference genome to subject genome 730s SNPs introduced: 13 730s Reference gaps introduced: 0 730s Read gaps introduced: 0 730s Rearrangements introduced: 0 730s Created read sampler 730s Sampling 28 reads 730s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 730s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 730s parsing sequence Sim.pm.1... 730s parsing sequence Sim.pm.2... 730s Parsed 40 reference bases 730s *** Run 72 of 100 730s /usr/bin/bowtie2 --trim3 2 --nofw -i L,0.114007456316908,3.70199505736566 --rfg 26.3014850335318,19.6042858866809 --trim5 6 --cp-ival 1 --score-min L,4.05906226859442,3.23818627383832 --ma 39.9868465386713 --rdg 28.7606072228642,8.86520324952075 --large-index --np 4 --cp-min 2 -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq 730s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 730s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 730s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 730s Warning: skipping mate #2 of read '8' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 730s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 730s Warning: skipping mate #1 of read '10' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 730s Warning: skipping mate #1 of read '11' because length (1) <= # seed mismatches (0) 730s Warning: skipping mate #1 of read '11' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 730s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 730s Warning: skipping mate #1 of read '16' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 730s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 730s Warning: skipping mate #1 of read '19' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 730s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 730s Warning: skipping mate #1 of read '25' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 730s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 730s Warning: skipping mate #1 of read '27' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 730s 28 reads; of these: 730s 22 (78.57%) were paired; of these: 730s 22 (100.00%) aligned concordantly 0 times 730s 0 (0.00%) aligned concordantly exactly 1 time 730s 0 (0.00%) aligned concordantly >1 times 730s ---- 730s 22 pairs aligned concordantly 0 times; of these: 730s 0 (0.00%) aligned discordantly 1 time 730s ---- 730s 22 pairs aligned 0 times concordantly or discordantly; of these: 730s 44 mates make up the pairs; of these: 730s 42 (95.45%) aligned 0 times 730s 2 (4.55%) aligned exactly 1 time 730s 0 (0.00%) aligned >1 times 730s 6 (21.43%) were unpaired; of these: 730s 6 (100.00%) aligned 0 times 730s 0 (0.00%) aligned exactly 1 time 730s 0 (0.00%) aligned >1 times 730s 4.00% overall alignment rate 730s Read 50 alignments... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s CGCGAGG 730s CGCGAGG 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s CTTCGCGAG 730s CTTCGCGAG 730s Processing line... 730s Processing line... 730s Processing line... 730s --- Summary --- 730s Read 1 reference strings 730s Checked 2 alignments, 0 edits 730s --------------- 730s PASSED 730s Flattened IUPAC characters 730s Mutating sequence Sim.pm.2 730s Introducing 6 SNPs, 0/0 ref/read gaps, and 2 rearrangements 730s Finished SNPs 730s Finished ref gaps 730s Finished read gaps 730s Mutating sequence Sim.pm.1 730s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 730s Finished SNPs 730s Finished ref gaps 730s Finished read gaps 730s Mutated reference genome to subject genome 730s SNPs introduced: 6 730s Reference gaps introduced: 1 730s Read gaps introduced: 0 730s Rearrangements introduced: 2 730s Created read sampler 730s Sampling 24 reads 730s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 730s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 730s parsing sequence Sim.pm.1... 730s parsing sequence Sim.pm.2... 730s Parsed 40 reference bases 730s *** Run 73 of 100 730s /usr/bin/bowtie2 --cp-ival 2 --local --trim5 6 --rfg 34.2325455717586 --mp 8.86810043770286,2.01776273805175 -N 0 -L27 --trim3 6 --large-index --cp-min 3 --np 2 --mm -R 1 --score-min L,2.13316626070027,4.17457942889969 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 730s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 730s Warning: skipping read '1' because it was < 2 characters long 730s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '2' because it was < 2 characters long 730s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 730s Warning: skipping read '3' because it was < 2 characters long 730s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '5' because it was < 2 characters long 730s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '11' because it was < 2 characters long 730s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '17' because it was < 2 characters long 730s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '18' because it was < 2 characters long 730s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '19' because it was < 2 characters long 730s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 730s Warning: skipping read '22' because it was < 2 characters long 730s /usr/bin/bowtie2 --cp-ival 2 --local --trim5 6 --rfg 34.2325455717586 --mp 8.86810043770286,2.01776273805175 -N 0 -L27 --trim3 6 --large-index --cp-min 3 --np 2 --mm -R 1 --score-min L,2.13316626070027,4.17457942889969 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 730s 24 reads; of these: 730s 24 (100.00%) were unpaired; of these: 730s 24 (100.00%) aligned 0 times 730s 0 (0.00%) aligned exactly 1 time 730s 0 (0.00%) aligned >1 times 730s 0.00% overall alignment rate 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s --- Summary --- 730s Read 1 reference strings 730s Checked 0 alignments, 0 edits 730s --------------- 730s PASSED 730s ALSO checking that bowtie2 and bowtie2-align match up 730s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 730s Warning: skipping read '1' because it was < 2 characters long 730s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '2' because it was < 2 characters long 730s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 730s Warning: skipping read '3' because it was < 2 characters long 730s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '5' because it was < 2 characters long 730s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '11' because it was < 2 characters long 730s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '17' because it was < 2 characters long 730s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '18' because it was < 2 characters long 730s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '19' because it was < 2 characters long 730s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 730s Warning: skipping read '22' because it was < 2 characters long 730s 24 reads; of these: 730s 24 (100.00%) were unpaired; of these: 730s 24 (100.00%) aligned 0 times 730s 0 (0.00%) aligned exactly 1 time 730s 0 (0.00%) aligned >1 times 730s 0.00% overall alignment rate 730s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 730s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 730s /usr/bin/bowtie2 --cp-ival 2 --local --trim5 6 --rfg 34.2325455717586 --mp 8.86810043770286,2.01776273805175 -N 0 -L27 --trim3 6 --large-index --cp-min 3 --np 2 --mm -R 1 --score-min L,2.13316626070027,4.17457942889969 -q -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 730s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 730s Warning: skipping read '1' because it was < 2 characters long 730s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '2' because it was < 2 characters long 730s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 730s Warning: skipping read '3' because it was < 2 characters long 730s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '5' because it was < 2 characters long 730s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '11' because it was < 2 characters long 730s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '17' because it was < 2 characters long 730s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '18' because it was < 2 characters long 730s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 730s Warning: skipping read '19' because it was < 2 characters long 730s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 730s Warning: skipping read '22' because it was < 2 characters long 730s 24 reads; of these: 730s 24 (100.00%) were unpaired; of these: 730s 24 (100.00%) aligned 0 times 730s 0 (0.00%) aligned exactly 1 time 730s 0 (0.00%) aligned >1 times 730s 0.00% overall alignment rate 730s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 730s Flattened IUPAC characters 730s Mutating sequence Sim.pm.2 730s Introducing 7 SNPs, 1/2 ref/read gaps, and 0 rearrangements 730s Finished SNPs 730s Finished ref gaps 730s Finished read gaps 730s Mutating sequence Sim.pm.1 730s Introducing 11 SNPs, 3/3 ref/read gaps, and 2 rearrangements 730s Finished SNPs 730s Finished ref gaps 730s Finished read gaps 730s Mutated reference genome to subject genome 730s SNPs introduced: 18 730s Reference gaps introduced: 4 730s Read gaps introduced: 5 730s Rearrangements introduced: 2 730s Created read sampler 730s Sampling 46 reads 730s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 730s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 730s parsing sequence Sim.pm.1... 730s parsing sequence Sim.pm.2... 730s Parsed 40 reference bases 730s *** Run 74 of 100 730s /usr/bin/bowtie2 -i C,4.37025595524896 -R 3 --score-min L,1.09405336854725,8.11203949410625 --rdg 36.0289444995393 --trim5 3 --large-index -a --cp-min 2 --cp-ival 1 --local --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq 730s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 730s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 730s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 730s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 730s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 730s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 730s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 730s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 730s 46 reads; of these: 730s 46 (100.00%) were paired; of these: 730s 46 (100.00%) aligned concordantly 0 times 730s 0 (0.00%) aligned concordantly exactly 1 time 730s 0 (0.00%) aligned concordantly >1 times 730s ---- 730s 46 pairs aligned concordantly 0 times; of these: 730s 0 (0.00%) aligned discordantly 1 time 730s ---- 730s 46 pairs aligned 0 times concordantly or discordantly; of these: 730s 92 mates make up the pairs; of these: 730s 92 (100.00%) aligned 0 times 730s 0 (0.00%) aligned exactly 1 time 730s 0 (0.00%) aligned >1 times 730s 0.00% overall alignment rate 730s Read 50 alignments... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s --- Summary --- 730s Read 1 reference strings 730s Checked 0 alignments, 0 edits 730s --------------- 730s PASSED 730s Flattened IUPAC characters 730s Mutating sequence Sim.pm.1 730s Introducing 9 SNPs, 0/1 ref/read gaps, and 1 rearrangements 730s Finished SNPs 730s Finished ref gaps 730s Finished read gaps 730s Mutating sequence Sim.pm.2 730s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 730s Finished SNPs 730s Finished ref gaps 730s Finished read gaps 730s Mutated reference genome to subject genome 730s SNPs introduced: 12 730s Reference gaps introduced: 0 730s Read gaps introduced: 1 730s Rearrangements introduced: 1 730s Created read sampler 730s Sampling 22 reads 730s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 730s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 730s parsing sequence Sim.pm.1... 730s parsing sequence Sim.pm.2... 730s Parsed 40 reference bases 730s *** Run 75 of 100 730s /usr/bin/bowtie2 --cp-ival 4 --cp-min 2 --large-index -M 4 --mm --score-min L,9.85122505591909,8.86023234488431 --gbar 2 -r -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.raw -2 /tmp/Sim.pm.qtk7xXsv_2.raw 730s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 730s Warning: skipping mate #2 of read '0' because length (1) <= # seed mismatches (0) 730s Warning: skipping mate #2 of read '0' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 730s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 730s Warning: skipping mate #1 of read '7' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 730s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 730s Warning: skipping mate #1 of read '9' because it was < 2 characters long 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 730s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 730s 22 reads; of these: 730s 22 (100.00%) were paired; of these: 730s 22 (100.00%) aligned concordantly 0 times 730s 0 (0.00%) aligned concordantly exactly 1 time 730s 0 (0.00%) aligned concordantly >1 times 730s ---- 730s 22 pairs aligned concordantly 0 times; of these: 730s 0 (0.00%) aligned discordantly 1 time 730s ---- 730s 22 pairs aligned 0 times concordantly or discordantly; of these: 730s 44 mates make up the pairs; of these: 730s 43 (97.73%) aligned 0 times 730s 0 (0.00%) aligned exactly 1 time 730s 1 (2.27%) aligned >1 times 730s 2.27% overall alignment rate 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s AC 730s AC 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 730s Processing line... 731s --- Summary --- 731s Read 1 reference strings 731s Checked 1 alignments, 0 edits 731s --------------- 731s PASSED 731s Flattened IUPAC characters 731s Mutating sequence Sim.pm.2 731s Introducing 5 SNPs, 2/0 ref/read gaps, and 1 rearrangements 731s Finished SNPs 731s Finished ref gaps 731s Finished read gaps 731s Mutating sequence Sim.pm.1 731s Introducing 15 SNPs, 0/0 ref/read gaps, and 0 rearrangements 731s Finished SNPs 731s Finished ref gaps 731s Finished read gaps 731s Mutated reference genome to subject genome 731s SNPs introduced: 20 731s Reference gaps introduced: 2 731s Read gaps introduced: 0 731s Rearrangements introduced: 1 731s Created read sampler 731s Sampling 69 reads 731s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 731s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 731s parsing sequence Sim.pm.1... 731s parsing sequence Sim.pm.2... 731s *** Run 76 of 100 731s /usr/bin/bowtie2 --trim3 0 --nofw --rfg 10.1280286027502 --n-ceil 0.148657166462326,0.451240635642528 --local --cp-ival 1 --score-min L,5.72979331064617,9.65534857087984 -R 1 --large-index --cp-min 3 --np 8 -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 731s Parsed 40 reference bases 731s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 731s Warning: skipping mate #2 of read '8' because it was < 2 characters long 731s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '15' because it was < 2 characters long 731s Read 50 alignments... 731s Read 100 alignments... 731s 69 reads; of these: 731s 69 (100.00%) were paired; of these: 731s 69 (100.00%) aligned concordantly 0 times 731s 0 (0.00%) aligned concordantly exactly 1 time 731s 0 (0.00%) aligned concordantly >1 times 731s ---- 731s 69 pairs aligned concordantly 0 times; of these: 731s 0 (0.00%) aligned discordantly 1 time 731s ---- 731s 69 pairs aligned 0 times concordantly or discordantly; of these: 731s 138 mates make up the pairs; of these: 731s 138 (100.00%) aligned 0 times 731s 0 (0.00%) aligned exactly 1 time 731s 0 (0.00%) aligned >1 times 731s 0.00% overall alignment rate 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s --- Summary --- 731s Read 1 reference strings 731s Checked 0 alignments, 0 edits 731s --------------- 731s PASSED 731s Flattened IUPAC characters 731s Mutating sequence Sim.pm.2 731s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 731s Finished SNPs 731s Finished ref gaps 731s Finished read gaps 731s Mutating sequence Sim.pm.1 731s Introducing 15 SNPs, 0/2 ref/read gaps, and 0 rearrangements 731s Finished SNPs 731s Finished ref gaps 731s Finished read gaps 731s Mutated reference genome to subject genome 731s SNPs introduced: 23 731s Reference gaps introduced: 0 731s *** Run 77 of 100 731s /usr/bin/bowtie2 --trim5 3 --local --cp-ival 1 --mp 4.07998976940249,2.26925378986009 --rfg 34.531028452859,18.2142403876458 --large-index --cp-min 5 --score-min L,9.49628094685445,8.780594178173 -D 39 --gbar 4 --rdg 30.7417690525997,1.38869811829149 --mm --qseq -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.qseq 731s Read gaps introduced: 2 731s Rearrangements introduced: 0 731s Created read sampler 731s Sampling 38 reads 731s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 731s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 731s parsing sequence Sim.pm.1... 731s parsing sequence Sim.pm.2... 731s Parsed 40 reference bases 731s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 731s 38 reads; of these: 731s 38 (100.00%) were unpaired; of these: 731s 38 (100.00%) aligned 0 times 731s 0 (0.00%) aligned exactly 1 time 731s 0 (0.00%) aligned >1 times 731s 0.00% overall alignment rate 731s /usr/bin/bowtie2 --trim5 3 --local --cp-ival 1 --mp 4.07998976940249,2.26925378986009 --rfg 34.531028452859,18.2142403876458 --large-index --cp-min 5 --score-min L,9.49628094685445,8.780594178173 -D 39 --gbar 4 --rdg 30.7417690525997,1.38869811829149 --mm --qseq -p 4 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s --- Summary --- 731s Read 1 reference strings 731s Checked 0 alignments, 0 edits 731s --------------- 731s PASSED 731s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 731s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 731s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 731s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 731s 38 reads; of these: 731s 38 (100.00%) were unpaired; of these: 731s 38 (100.00%) aligned 0 times 731s 0 (0.00%) aligned exactly 1 time 731s 0 (0.00%) aligned >1 times 731s 0.00% overall alignment rate 731s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 731s Flattened IUPAC characters 731s Mutating sequence Sim.pm.1 731s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 731s Finished SNPs 731s Finished ref gaps 731s Finished read gaps 731s Mutating sequence Sim.pm.2 731s Introducing 4 SNPs, 0/1 ref/read gaps, and 1 rearrangements 731s Finished SNPs 731s Finished ref gaps 731s Finished read gaps 731s Mutated reference genome to subject genome 731s SNPs introduced: 6 731s Reference gaps introduced: 0 731s Read gaps introduced: 2 731s Rearrangements introduced: 1 731s Created read sampler 731s Sampling 110 reads 731s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 731s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 731s parsing sequence Sim.pm.1... 731s *** Run 78 of 100 731s /usr/bin/bowtie2 --mm --rdg 46.227719417939,12.5113168062931 -k 2 --score-min L,2.25192211308208,6.49372839041376 --nofw --trim3 6 --cp-ival 1 --trim5 3 --n-ceil 0.531580795154147,1.34928001774885 --large-index --cp-min 3 -r -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.raw -2 /tmp/Sim.pm.qtk7xXsv_2.raw 731s parsing sequence Sim.pm.2... 731s Parsed 40 reference bases 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 731s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 731s Warning: skipping read '6' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 731s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '9' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 731s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '14' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 731s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '18' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 731s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 731s Warning: skipping read '22' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 731s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '24' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 731s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '40' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 731s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '41' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 731s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 731s Warning: skipping read '44' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 731s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '48' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 731s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '49' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 731s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '50' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 731s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 731s Warning: skipping read '56' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 731s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '58' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 731s Read 50 alignments... 731s Read 100 alignments... 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 731s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '65' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 731s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '77' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 731s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '81' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 731s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '92' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 731s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 731s Warning: skipping mate #1 of read '97' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 731s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 731s Warning: skipping read '99' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 731s 110 reads; of these: 731s 83 (75.45%) were paired; of these: 731s 83 (100.00%) aligned concordantly 0 times 731s 0 (0.00%) aligned concordantly exactly 1 time 731s 0 (0.00%) aligned concordantly >1 times 731s ---- 731s 83 pairs aligned concordantly 0 times; of these: 731s 0 (0.00%) aligned discordantly 1 time 731s ---- 731s 83 pairs aligned 0 times concordantly or discordantly; of these: 731s 166 mates make up the pairs; of these: 731s 158 (95.18%) aligned 0 times 731s 5 (3.01%) aligned exactly 1 time 731s 3 (1.81%) aligned >1 times 731s 27 (24.55%) were unpaired; of these: 731s 26 (96.30%) aligned 0 times 731s 1 (3.70%) aligned exactly 1 time 731s 0 (0.00%) aligned >1 times 731s 4.66% overall alignment rate 731s Read 150 alignments... 731s Read 200 alignments... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s CG 731s CG 731s Processing line... 731s CG 731s CG 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s CGAGGAGGAG 731s CGAGGAGGAG 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s TTCGCGAGGAGGAG 731s TTCGCGAGGAGGAG 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s GCGAGGAGGA 731s GCGAGGAGGA 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s GCCG 731s GCCG 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s AT 731s AT 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s GC 731s GC 731s Processing line... 731s GC 731s GC 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s GGG 731s GGG 731s Processing line... 731s GGG 731s GGG 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s ATC 731s ATC 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s --- Summary --- 731s Read 1 reference strings 731s Checked 12 alignments, 0 edits 731s --------------- 731s PASSED 731s Flattened IUPAC characters 731s Mutating sequence Sim.pm.1 731s Introducing 11 SNPs, 0/1 ref/read gaps, and 1 rearrangements 731s Finished SNPs 731s Finished ref gaps 731s Finished read gaps 731s Mutating sequence Sim.pm.2 731s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 731s Finished SNPs 731s Finished ref gaps 731s Finished read gaps 731s Mutated reference genome to subject genome 731s SNPs introduced: 14 731s Reference gaps introduced: 0 731s Read gaps introduced: 1 731s Rearrangements introduced: 1 731s Created read sampler 731s Sampling 101 reads 731s *** Run 79 of 100 731s /usr/bin/bowtie2 --ma 27.4260701221488 --score-min L,1.07616899324319,3.49024665806022 -R 3 --mp 6.87601253365216,6.32178569741165 --mm --cp-min 4 --large-index -M 6 --n-ceil 0.378484608918052,0.659403383289132 --cp-ival 1 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 731s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 731s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 731s parsing sequence Sim.pm.1... 731s parsing sequence Sim.pm.2... 731s Parsed 40 reference bases 731s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 731s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 731s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 731s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 731s Warning: skipping read '2' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 731s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 731s Warning: skipping read '58' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 731s 101 reads; of these: 731s 101 (100.00%) were unpaired; of these: 731s 90 (89.11%) aligned 0 times 731s 4 (3.96%) aligned exactly 1 time 731s 7 (6.93%) aligned >1 times 731s 10.89% overall alignment rate 731s Read 50 alignments... 731s Read 100 alignments... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s GCCGG 731s GCCGG 731s Processing line... 731s Processing line... 731s CGACG 731s CGACG 731s Processing line... 731s Processing line... 731s GCG 731s GCG 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s GCGA 731s GCGA 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s CATCT 731s CATCT 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s GC 731s GC 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s CG 731s CG 731s Processing line... 731s Processing line... 731s Processing line... 731s ATC 731s ATC 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s CCG 731s CCG 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s GGC 731s GGC 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s CG 731s CG 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s Processing line... 731s --- Summary --- 731s Read 1 reference strings 731s Checked 11 alignments, 0 edits 731s --------------- 731s PASSED 731s ALSO checking that bowtie2 and bowtie2-align match up 731s /usr/bin/bowtie2 --ma 27.4260701221488 --score-min L,1.07616899324319,3.49024665806022 -R 3 --mp 6.87601253365216,6.32178569741165 --mm --cp-min 4 --large-index -M 6 --n-ceil 0.378484608918052,0.659403383289132 --cp-ival 1 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 731s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 731s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 731s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 731s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 731s Warning: skipping read '2' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 731s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 731s Warning: skipping read '58' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 731s 101 reads; of these: 731s 101 (100.00%) were unpaired; of these: 731s 90 (89.11%) aligned 0 times 731s 4 (3.96%) aligned exactly 1 time 731s 7 (6.93%) aligned >1 times 731s 10.89% overall alignment rate 731s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 731s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 731s /usr/bin/bowtie2 --ma 27.4260701221488 --score-min L,1.07616899324319,3.49024665806022 -R 3 --mp 6.87601253365216,6.32178569741165 --mm --cp-min 4 --large-index -M 6 --n-ceil 0.378484608918052,0.659403383289132 --cp-ival 1 -q -p 4 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 731s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 731s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 731s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 731s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 731s Warning: skipping read '2' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 731s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 731s Warning: skipping read '58' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 731s 101 reads; of these: 731s 101 (100.00%) were unpaired; of these: 731s 90 (89.11%) aligned 0 times 731s 4 (3.96%) aligned exactly 1 time 731s 7 (6.93%) aligned >1 times 731s 10.89% overall alignment rate 731s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 731s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 731s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 731s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 731s /usr/bin/bowtie2 --ma 27.4260701221488 --score-min L,1.07616899324319,3.49024665806022 -R 3 --mp 6.87601253365216,6.32178569741165 --mm --cp-min 4 --large-index -M 6 --n-ceil 0.378484608918052,0.659403383289132 --cp-ival 1 -q -p 4 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 731s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 731s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 731s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 731s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 731s Warning: skipping read '2' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 731s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 731s Warning: skipping read '58' because it was < 2 characters long 731s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 731s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 732s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 732s 101 reads; of these: 732s 101 (100.00%) were unpaired; of these: 732s 90 (89.11%) aligned 0 times 732s 4 (3.96%) aligned exactly 1 time 732s 7 (6.93%) aligned >1 times 732s 10.89% overall alignment rate 732s Flattened IUPAC characters 732s Mutating sequence Sim.pm.2 732s Introducing 6 SNPs, 0/1 ref/read gaps, and 1 rearrangements 732s Finished SNPs 732s Finished ref gaps 732s Finished read gaps 732s Mutating sequence Sim.pm.1 732s Introducing 10 SNPs, 0/2 ref/read gaps, and 0 rearrangements 732s Finished SNPs 732s Finished ref gaps 732s Finished read gaps 732s Mutated reference genome to subject genome 732s *** Run 80 of 100 732s /usr/bin/bowtie2 --trim3 4 --score-min L,7.01591561844238,2.69114885607159 -N 1 -L30 --gbar 2 --rdg 5.00532880725942 --mm --rfg 12.8117981511181 --cp-min 3 --large-index -a --cp-ival 1 -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 732s SNPs introduced: 16 732s Reference gaps introduced: 0 732s Read gaps introduced: 3 732s Rearrangements introduced: 1 732s Created read sampler 732s Sampling 84 reads 732s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 732s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 732s parsing sequence Sim.pm.1... 732s parsing sequence Sim.pm.2... 732s Parsed 40 reference bases 732s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 732s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 732s Warning: skipping mate #1 of read '18' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 732s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (1) 732s Warning: skipping mate #1 of read '51' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 732s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (1) 732s Warning: skipping mate #1 of read '54' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 732s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (1) 732s Warning: skipping mate #1 of read '61' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 732s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (1) 732s Warning: skipping mate #1 of read '62' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 732s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (1) 732s Warning: skipping mate #1 of read '68' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 732s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (1) 732s Warning: skipping mate #1 of read '75' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 732s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (1) 732s Warning: skipping mate #1 of read '76' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 732s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (1) 732s Warning: skipping mate #1 of read '80' because it was < 2 characters long 732s Read 50 alignments... 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 732s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (1) 732s Warning: skipping mate #1 of read '84' because it was < 2 characters long 732s Read 100 alignments... 732s 84 reads; of these: 732s 78 (92.86%) were paired; of these: 732s 78 (100.00%) aligned concordantly 0 times 732s 0 (0.00%) aligned concordantly exactly 1 time 732s 0 (0.00%) aligned concordantly >1 times 732s ---- 732s 78 pairs aligned concordantly 0 times; of these: 732s 0 (0.00%) aligned discordantly 1 time 732s ---- 732s 78 pairs aligned 0 times concordantly or discordantly; of these: 732s 156 mates make up the pairs; of these: 732s 149 (95.51%) aligned 0 times 732s 3 (1.92%) aligned exactly 1 time 732s 4 (2.56%) aligned >1 times 732s 6 (7.14%) were unpaired; of these: 732s 6 (100.00%) aligned 0 times 732s 0 (0.00%) aligned exactly 1 time 732s 0 (0.00%) aligned >1 times 732s 4.32% overall alignment rate 732s Read 150 alignments... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s GGA 732s GGA 732s Processing line... 732s GGA 732s GGA 732s Processing line... 732s Processing line... 732s CC 732s CC 732s Processing line... 732s GG 732s GG 732s Processing line... 732s GG 732s GG 732s Processing line... 732s GG 732s GG 732s Processing line... 732s GG 732s GG 732s Processing line... 732s GG 732s GG 732s Processing line... 732s GG 732s GG 732s Processing line... 732s CC 732s CC 732s Processing line... 732s GG 732s GG 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s GCG 732s GCG 732s Processing line... 732s GCG 732s GCG 732s Processing line... 732s CGC 732s CGC 732s Processing line... 732s GCG 732s GCG 732s Processing line... 732s CGC 732s CGC 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s GCGAGGAG 732s GCGAGGAG 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s AG 732s AG 732s Processing line... 732s CT 732s CT 732s Processing line... 732s AG 732s AG 732s Processing line... 732s CT 732s CT 732s Processing line... 732s AG 732s AG 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s CTTCGCG 732s CTTCGCG 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s ACA 732s ACA 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s --- Summary --- 732s Read 1 reference strings 732s Checked 24 alignments, 0 edits 732s --------------- 732s PASSED 732s Flattened IUPAC characters 732s Mutating sequence Sim.pm.1 732s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 732s Finished SNPs 732s Finished ref gaps 732s Finished read gaps 732s Mutating sequence Sim.pm.2 732s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 732s Finished SNPs 732s Finished ref gaps 732s Finished read gaps 732s Mutated reference genome to subject genome 732s SNPs introduced: 8 732s Reference gaps introduced: 1 732s Read gaps introduced: 1 732s Rearrangements introduced: 1 732s Created read sampler 732s Sampling 13 reads 732s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 732s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 732s parsing sequence Sim.pm.1... 732s parsing sequence Sim.pm.2... 732s Parsed 40 reference bases 732s *** Run 81 of 100 732s /usr/bin/bowtie2 --mp 7.92460399241715,1.18548595894422 -N 1 -L14 --trim3 9 --cp-ival 1 --trim5 3 --norc --n-ceil 0.257633086479647,1.09549304382732 -a --rdg 47.0706714438308,2.13531772024092 --score-min L,6.02936941082422,3.85772238760553 --cp-min 2 --np 1 --large-index -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 732s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 732s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '1' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 732s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '2' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 732s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '5' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 732s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '7' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 732s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '9' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 732s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '13' because it was < 2 characters long 732s /usr/bin/bowtie2 --mp 7.92460399241715,1.18548595894422 -N 1 -L14 --trim3 9 --cp-ival 1 --trim5 3 --norc --n-ceil 0.257633086479647,1.09549304382732 -a --rdg 47.0706714438308,2.13531772024092 --score-min L,6.02936941082422,3.85772238760553 --cp-min 2 --np 1 --large-index -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 732s 13 reads; of these: 732s 13 (100.00%) were unpaired; of these: 732s 13 (100.00%) aligned 0 times 732s 0 (0.00%) aligned exactly 1 time 732s 0 (0.00%) aligned >1 times 732s 0.00% overall alignment rate 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s --- Summary --- 732s Read 1 reference strings 732s Checked 0 alignments, 0 edits 732s --------------- 732s PASSED 732s ALSO checking that bowtie2 and bowtie2-align match up 732s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 732s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '1' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 732s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '2' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 732s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '5' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 732s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '7' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 732s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '9' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 732s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '13' because it was < 2 characters long 732s 13 reads; of these: 732s 13 (100.00%) were unpaired; of these: 732s 13 (100.00%) aligned 0 times 732s 0 (0.00%) aligned exactly 1 time 732s 0 (0.00%) aligned >1 times 732s 0.00% overall alignment rate 732s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 732s /usr/bin/bowtie2 --mp 7.92460399241715,1.18548595894422 -N 1 -L14 --trim3 9 --cp-ival 1 --trim5 3 --norc --n-ceil 0.257633086479647,1.09549304382732 -a --rdg 47.0706714438308,2.13531772024092 --score-min L,6.02936941082422,3.85772238760553 --cp-min 2 --np 1 --large-index -q -p 2 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 732s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 732s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 732s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '1' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 732s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '2' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 732s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '5' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 732s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '7' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 732s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '9' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 732s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 732s Warning: skipping read '13' because it was < 2 characters long 732s 13 reads; of these: 732s 13 (100.00%) were unpaired; of these: 732s 13 (100.00%) aligned 0 times 732s 0 (0.00%) aligned exactly 1 time 732s 0 (0.00%) aligned >1 times 732s 0.00% overall alignment rate 732s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 732s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 732s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 732s Flattened IUPAC characters 732s Mutating sequence Sim.pm.1 732s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 732s Finished SNPs 732s Finished ref gaps 732s Finished read gaps 732s Mutating sequence Sim.pm.2 732s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 732s Finished SNPs 732s Finished ref gaps 732s Finished read gaps 732s Mutated reference genome to subject genome 732s SNPs introduced: 5 732s Reference gaps introduced: 0 732s Read gaps introduced: 0 732s Rearrangements introduced: 0 732s Created read sampler 732s Sampling 33 reads 732s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 732s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 732s parsing sequence Sim.pm.1... 732s parsing sequence Sim.pm.2... 732s Parsed 40 reference bases 732s *** Run 82 of 100 732s /usr/bin/bowtie2 --cp-ival 3 --trim5 7 --trim3 4 --nofw -N 0 -L17 --large-index --np 7 --cp-min 5 --mm --score-min L,9.72708007544363,7.81187057542103 -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 732s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 732s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 732s Warning: skipping read '2' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 732s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 732s Warning: skipping read '3' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 732s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 732s Warning: skipping read '5' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 732s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 732s Warning: skipping read '7' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 732s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 732s Warning: skipping read '13' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 732s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 732s Warning: skipping read '20' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 732s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 732s Warning: skipping read '21' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 732s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 732s Warning: skipping read '25' because it was < 2 characters long 732s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 732s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 732s 33 reads; of these: 732s 33 (100.00%) were unpaired; of these: 732s 32 (96.97%) aligned 0 times 732s 1 (3.03%) aligned exactly 1 time 732s 0 (0.00%) aligned >1 times 732s 3.03% overall alignment rate 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s CCGGGGGC 732s CCGGGGGC 732s Processing line... 732s Processing line... 732s --- Summary --- 732s Read 1 reference strings 732s Checked 1 alignments, 0 edits 732s --------------- 732s PASSED 732s Flattened IUPAC characters 732s Mutating sequence Sim.pm.1 732s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 732s Finished SNPs 732s Finished ref gaps 732s Finished read gaps 732s Mutating sequence Sim.pm.2 732s Introducing 6 SNPs, 0/0 ref/read gaps, and 2 rearrangements 732s Finished SNPs 732s Finished ref gaps 732s Finished read gaps 732s Mutated reference genome to subject genome 732s SNPs introduced: 6 732s Reference gaps introduced: 0 732s Read gaps introduced: 0 732s Rearrangements introduced: 2 732s Created read sampler 732s Sampling 68 reads 732s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 732s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 732s parsing sequence Sim.pm.1... 732s parsing sequence Sim.pm.2... 732s Parsed 40 reference bases 732s *** Run 83 of 100 732s /usr/bin/bowtie2 --nofw --trim3 3 --score-min L,1.17456729749135,3.50760836300753 --mp 9.36520459318645,3.91305973968007 -D 14 --rfg 30.511759056011 --cp-min 4 --large-index --trim5 4 --local --cp-ival 1 -r -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.raw -2 /tmp/Sim.pm.qtk7xXsv_2.raw 732s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 732s Warning: skipping mate #2 of read '2' because it was < 2 characters long 732s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 732s Warning: skipping mate #2 of read '3' because it was < 2 characters long 732s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 732s Warning: skipping mate #1 of read '10' because it was < 2 characters long 732s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 732s Warning: skipping mate #1 of read '17' because it was < 2 characters long 732s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 732s Warning: skipping mate #2 of read '25' because it was < 2 characters long 732s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 732s Warning: skipping mate #1 of read '31' because it was < 2 characters long 732s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 732s Warning: skipping mate #1 of read '34' because it was < 2 characters long 732s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 732s Warning: skipping mate #1 of read '40' because it was < 2 characters long 732s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 732s Warning: skipping mate #1 of read '42' because it was < 2 characters long 732s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 732s Warning: skipping mate #1 of read '47' because it was < 2 characters long 732s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (0) 732s Warning: skipping mate #1 of read '49' because it was < 2 characters long 732s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 732s Warning: skipping mate #1 of read '56' because it was < 2 characters long 732s Read 50 alignments... 732s 68 reads; of these: 732s 59 (86.76%) were paired; of these: 732s 59 (100.00%) aligned concordantly 0 times 732s 0 (0.00%) aligned concordantly exactly 1 time 732s 0 (0.00%) aligned concordantly >1 times 732s ---- 732s 59 pairs aligned concordantly 0 times; of these: 732s 0 (0.00%) aligned discordantly 1 time 732s ---- 732s 59 pairs aligned 0 times concordantly or discordantly; of these: 732s 118 mates make up the pairs; of these: 732s 118 (100.00%) aligned 0 times 732s 0 (0.00%) aligned exactly 1 time 732s 0 (0.00%) aligned >1 times 732s 9 (13.24%) were unpaired; of these: 732s 9 (100.00%) aligned 0 times 732s 0 (0.00%) aligned exactly 1 time 732s 0 (0.00%) aligned >1 times 732s 0.00% overall alignment rate 732s Read 100 alignments... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s Processing line... 732s --- Summary --- 732s Read 1 reference strings 732s Checked 0 alignments, 0 edits 732s --------------- 732s PASSED 732s Flattened IUPAC characters 732s Mutating sequence Sim.pm.2 732s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 732s Finished SNPs 732s Finished ref gaps 732s Finished read gaps 732s Mutating sequence Sim.pm.1 732s Introducing 10 SNPs, 2/1 ref/read gaps, and 0 rearrangements 732s Finished SNPs 732s Finished ref gaps 732s Finished read gaps 732s Mutated reference genome to subject genome 732s SNPs introduced: 11 732s Reference gaps introduced: 2 732s Read gaps introduced: 2 732s Rearrangements introduced: 0 732s Created read sampler 732s Sampling 49 reads 732s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 732s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 732s parsing sequence Sim.pm.1... 732s parsing sequence Sim.pm.2... 732s Parsed 40 reference bases 732s *** Run 84 of 100 732s /usr/bin/bowtie2 --mp 7.13133541036561,1.36616076395086 -i C,3.19903025027251,1.5450283174065 -N 1 -L20 --score-min L,9.47538598878673,9.62131393552371 --rfg 20.6561628448655 --trim5 1 --cp-min 3 --large-index --cp-ival 3 --local -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw 733s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '20' because it was < 2 characters long 733s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '39' because it was < 2 characters long 733s 49 reads; of these: 733s 49 (100.00%) were unpaired; of these: 733s 49 (100.00%) aligned 0 times 733s 0 (0.00%) aligned exactly 1 time 733s 0 (0.00%) aligned >1 times 733s 0.00% overall alignment rate 733s Read 50 alignments... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s --- Summary --- 733s Read 1 reference strings 733s Checked 0 alignments, 0 edits 733s --------------- 733s PASSED 733s ALSO checking that bowtie2 and bowtie2-align match up 733s /usr/bin/bowtie2 --mp 7.13133541036561,1.36616076395086 -i C,3.19903025027251,1.5450283174065 -N 1 -L20 --score-min L,9.47538598878673,9.62131393552371 --rfg 20.6561628448655 --trim5 1 --cp-min 3 --large-index --cp-ival 3 --local -r -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 733s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '20' because it was < 2 characters long 733s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '39' because it was < 2 characters long 733s 49 reads; of these: 733s 49 (100.00%) were unpaired; of these: 733s 49 (100.00%) aligned 0 times 733s 0 (0.00%) aligned exactly 1 time 733s 0 (0.00%) aligned >1 times 733s 0.00% overall alignment rate 733s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 733s Flattened IUPAC characters 733s Mutating sequence Sim.pm.1 733s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 733s Finished SNPs 733s Finished ref gaps 733s Finished read gaps 733s Mutating sequence Sim.pm.2 733s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 733s Finished SNPs 733s Finished ref gaps 733s Finished read gaps 733s Mutated reference genome to subject genome 733s SNPs introduced: 8 733s Reference gaps introduced: 0 733s Read gaps introduced: 2 733s Rearrangements introduced: 0 733s Created read sampler 733s Sampling 172 reads 733s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 733s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 733s parsing sequence Sim.pm.1... 733s *** Run 85 of 100 733s /usr/bin/bowtie2 --cp-ival 1 -M 5 --norc --trim5 7 --trim3 6 --nofw -N 1 -L23 --mp 2.62046078114732,1.5608854413383 -i S,2.79534086426905 --np 1 --cp-min 2 --large-index --score-min L,6.5208907408061,2.32207451312632 -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta 733s parsing sequence Sim.pm.2... 733s Parsed 40 reference bases 733s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 733s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 733s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '2' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 733s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '5' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 733s Warning: skipping read '8' because length (1) <= # seed mismatches (1) 733s Warning: skipping read '8' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 733s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '11' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 733s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '12' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 733s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '14' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 733s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '16' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 733s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '18' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 733s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '20' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 733s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '29' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 733s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '31' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 733s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '32' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 733s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '34' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 733s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '37' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 733s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '39' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 733s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '42' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 733s Warning: skipping read '50' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '50' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 733s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '52' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 733s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '53' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 733s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '54' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 733s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '55' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 733s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '56' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 733s Warning: skipping read '61' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '61' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 733s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '62' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 733s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '63' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 733s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '68' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 733s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '73' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 733s Warning: skipping read '76' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '76' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 733s Warning: skipping read '78' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '78' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 733s Warning: skipping read '79' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '79' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 733s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '80' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 733s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '81' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 733s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '83' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 733s Warning: skipping read '87' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '87' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 733s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '88' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 733s Warning: skipping read '89' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '89' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 733s Warning: skipping read '91' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '91' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 733s Warning: skipping read '95' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '95' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 733s Warning: skipping read '96' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '96' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 733s Warning: skipping read '97' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '97' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 733s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '99' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 733s Warning: skipping read '104' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '104' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 733s Warning: skipping read '109' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '109' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 733s Warning: skipping read '110' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '110' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 733s Warning: skipping read '111' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '111' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 733s Warning: skipping read '117' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '117' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 733s Warning: skipping read '118' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '118' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 733s Warning: skipping read '126' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '126' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 733s Warning: skipping read '129' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '129' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 733s Warning: skipping read '131' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '131' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 733s Warning: skipping read '132' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '132' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 733s Warning: skipping read '133' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '133' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 733s Warning: skipping read '136' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '136' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 733s Warning: skipping read '139' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '139' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 733s Warning: skipping read '140' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '140' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 733s Warning: skipping read '144' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '144' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 733s Warning: skipping read '150' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '150' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 733s Warning: skipping read '165' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '165' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 733s 172 reads; of these: 733s 172 (100.00%) were unpaired; of these: 733s 172 (100.00%) aligned 0 times 733s 0 (0.00%) aligned exactly 1 time 733s 0 (0.00%) aligned >1 times 733s 0.00% overall alignment rate 733s Read 50 alignments... 733s Read 100 alignments... 733s Read 150 alignments... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s --- Summary --- 733s Read 1 reference strings 733s Checked 0 alignments, 0 edits 733s /usr/bin/bowtie2 --cp-ival 1 -M 5 --norc --trim5 7 --trim3 6 --nofw -N 1 -L23 --mp 2.62046078114732,1.5608854413383 -i S,2.79534086426905 --np 1 --cp-min 2 --large-index --score-min L,6.5208907408061,2.32207451312632 -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 733s --------------- 733s PASSED 733s ALSO checking that bowtie2 and bowtie2-align match up 733s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 733s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 733s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '2' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 733s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '5' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 733s Warning: skipping read '8' because length (1) <= # seed mismatches (1) 733s Warning: skipping read '8' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 733s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '11' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 733s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '12' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 733s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '14' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 733s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '16' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 733s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '18' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 733s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '20' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 733s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '29' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 733s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '31' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 733s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '32' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 733s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '34' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 733s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '37' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 733s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '39' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 733s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '42' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 733s Warning: skipping read '50' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '50' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 733s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '52' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 733s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '53' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 733s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '54' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 733s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '55' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 733s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '56' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 733s Warning: skipping read '61' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '61' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 733s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '62' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 733s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '63' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 733s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '68' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 733s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '73' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 733s Warning: skipping read '76' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '76' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 733s Warning: skipping read '78' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '78' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 733s Warning: skipping read '79' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '79' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 733s Warning: skipping read '80' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '80' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 733s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '81' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 733s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '83' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 733s Warning: skipping read '87' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '87' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 733s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '88' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 733s Warning: skipping read '89' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '89' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 733s Warning: skipping read '91' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '91' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 733s Warning: skipping read '95' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '95' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 733s Warning: skipping read '96' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '96' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 733s Warning: skipping read '97' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '97' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 733s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '99' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 733s Warning: skipping read '104' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '104' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 733s Warning: skipping read '109' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '109' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 733s Warning: skipping read '110' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '110' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 733s Warning: skipping read '111' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '111' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 733s Warning: skipping read '117' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '117' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 733s Warning: skipping read '118' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '118' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 733s Warning: skipping read '126' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '126' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 733s Warning: skipping read '129' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '129' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 733s Warning: skipping read '131' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '131' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 733s Warning: skipping read '132' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '132' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 733s Warning: skipping read '133' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '133' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 733s Warning: skipping read '136' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '136' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 733s Warning: skipping read '139' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '139' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 733s Warning: skipping read '140' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '140' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 733s Warning: skipping read '144' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '144' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 733s Warning: skipping read '150' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '150' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 733s Warning: skipping read '165' because length (0) <= # seed mismatches (1) 733s Warning: skipping read '165' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 733s 172 reads; of these: 733s 172 (100.00%) were unpaired; of these: 733s 172 (100.00%) aligned 0 times 733s 0 (0.00%) aligned exactly 1 time 733s 0 (0.00%) aligned >1 times 733s 0.00% overall alignment rate 733s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 733s Flattened IUPAC characters 733s Mutating sequence Sim.pm.2 733s Introducing 6 SNPs, 0/1 ref/read gaps, and 1 rearrangements 733s Finished SNPs 733s Finished ref gaps 733s Finished read gaps 733s Mutating sequence Sim.pm.1 733s Introducing 13 SNPs, 0/1 ref/read gaps, and 0 rearrangements 733s Finished SNPs 733s Finished ref gaps 733s Finished read gaps 733s Mutated reference genome to subject genome 733s SNPs introduced: 19 733s Reference gaps introduced: 0 733s Read gaps introduced: 2 733s Rearrangements introduced: 1 733s Created read sampler 733s Sampling 152 reads 733s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 733s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 733s parsing sequence Sim.pm.1... 733s parsing sequence Sim.pm.2... 733s *** Run 86 of 100 733s /usr/bin/bowtie2 --large-index --np 1 --cp-min 8 --rdg 8.00513106046065,13.3667117497746 --gbar 4 -D 45 --score-min L,8.58729910148327,8.42791174974875 --ma 26.578532833222 --cp-ival 1 --trim5 5 --trim3 8 --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq 733s Parsed 40 reference bases 733s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 733s Warning: skipping mate #2 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #2 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 733s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 733s Read 50 alignments... 733s Read 100 alignments... 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #2 of read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 733s Warning: skipping mate #2 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 733s Read 150 alignments... 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 733s Warning: skipping mate #2 of read 'R_1_1_1_139_139_1/1' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #2 of read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 733s Read 200 alignments... 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_149_149_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_149_149_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_151_151_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 733s 152 reads; of these: 733s 113 (74.34%) were paired; of these: 733s 113 (100.00%) aligned concordantly 0 times 733s 0 (0.00%) aligned concordantly exactly 1 time 733s 0 (0.00%) aligned concordantly >1 times 733s ---- 733s 113 pairs aligned concordantly 0 times; of these: 733s 0 (0.00%) aligned discordantly 1 time 733s ---- 733s 113 pairs aligned 0 times concordantly or discordantly; of these: 733s 226 mates make up the pairs; of these: 733s 217 (96.02%) aligned 0 times 733s 3 (1.33%) aligned exactly 1 time 733s 6 (2.65%) aligned >1 times 733s 39 (25.66%) were unpaired; of these: 733s 37 (94.87%) aligned 0 times 733s 0 (0.00%) aligned exactly 1 time 733s 2 (5.13%) aligned >1 times 733s 4.15% overall alignment rate 733s Read 250 alignments... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s CG 733s CG 733s Processing line... 733s Processing line... 733s TC 733s TC 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s GGGG 733s GGGG 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s GGG 733s GGG 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s TG 733s TG 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s GCGCG 733s GCGCG 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s GCG 733s GCG 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s ATCTT 733s ATCTT 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s AC 733s AC 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s CGCG 733s CGCG 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s GCCGG 733s GCCGG 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s --- Summary --- 733s Read 1 reference strings 733s Checked 11 alignments, 0 edits 733s /usr/bin/bowtie2 --large-index --np 1 --cp-min 8 --rdg 8.00513106046065,13.3667117497746 --gbar 4 -D 45 --score-min L,8.58729910148327,8.42791174974875 --ma 26.578532833222 --cp-ival 1 --trim5 5 --trim3 8 --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 733s --------------- 733s PASSED 733s ALSO checking that bowtie2 and bowtie2-align match up 733s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 733s Warning: skipping mate #2 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #2 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 733s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #2 of read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 733s Warning: skipping mate #2 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 733s Warning: skipping mate #2 of read 'R_1_1_1_139_139_1/1' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #2 of read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 733s Warning: skipping read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_149_149_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_149_149_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 733s Warning: skipping mate #1 of read 'R_1_1_1_151_151_1/1' because length (0) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 733s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 733s 152 reads; of these: 733s 113 (74.34%) were paired; of these: 733s 113 (100.00%) aligned concordantly 0 times 733s 0 (0.00%) aligned concordantly exactly 1 time 733s 0 (0.00%) aligned concordantly >1 times 733s ---- 733s 113 pairs aligned concordantly 0 times; of these: 733s 0 (0.00%) aligned discordantly 1 time 733s ---- 733s 113 pairs aligned 0 times concordantly or discordantly; of these: 733s 226 mates make up the pairs; of these: 733s 217 (96.02%) aligned 0 times 733s 3 (1.33%) aligned exactly 1 time 733s 6 (2.65%) aligned >1 times 733s 39 (25.66%) were unpaired; of these: 733s 37 (94.87%) aligned 0 times 733s 0 (0.00%) aligned exactly 1 time 733s 2 (5.13%) aligned >1 times 733s 4.15% overall alignment rate 733s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 733s Flattened IUPAC characters 733s Mutating sequence Sim.pm.2 733s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 733s Finished SNPs 733s Finished ref gaps 733s Finished read gaps 733s Mutating sequence Sim.pm.1 733s Introducing 8 SNPs, 1/1 ref/read gaps, and 0 rearrangements 733s Finished SNPs 733s Finished ref gaps 733s Finished read gaps 733s Mutated reference genome to subject genome 733s SNPs introduced: 9 733s Reference gaps introduced: 1 733s Read gaps introduced: 1 733s Rearrangements introduced: 1 733s Created read sampler 733s Sampling 124 reads 733s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 733s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 733s parsing sequence Sim.pm.1... 733s parsing sequence Sim.pm.2... 733s *** Run 87 of 100 733s /usr/bin/bowtie2 -i L,0.395108470033957 --mp 8.55125433898374,6.31853686323186 --cp-ival 1 --local --trim5 0 --mm --rdg 5.70095371575144,17.2611525623118 --score-min L,2.15272600668562,6.82371897344297 --np 5 --cp-min 2 --large-index -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq 733s Parsed 40 reference bases 733s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #2 of read '5' because it was < 2 characters long 733s Warning: skipping mate #1 of read '10' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read '10' because it was < 2 characters long 733s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #1 of read '13' because it was < 2 characters long 733s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 733s Warning: skipping mate #2 of read '14' because it was < 2 characters long 733s Read 50 alignments... 733s Warning: skipping mate #2 of read '120' because length (1) <= # seed mismatches (0) 733s Read 100 alignments... 733s Read 150 alignments... 733s Warning: skipping mate #2 of read '120' because it was < 2 characters long 733s Read 200 alignments... 733s 124 reads; of these: 733s 124 (100.00%) were paired; of these: 733s 124 (100.00%) aligned concordantly 0 times 733s 0 (0.00%) aligned concordantly exactly 1 time 733s 0 (0.00%) aligned concordantly >1 times 733s ---- 733s 124 pairs aligned concordantly 0 times; of these: 733s 0 (0.00%) aligned discordantly 1 time 733s ---- 733s 124 pairs aligned 0 times concordantly or discordantly; of these: 733s 248 mates make up the pairs; of these: 733s 248 (100.00%) aligned 0 times 733s 0 (0.00%) aligned exactly 1 time 733s 0 (0.00%) aligned >1 times 733s 0.00% overall alignment rate 733s Read 250 alignments... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing 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Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s Processing line... 733s --- Summary --- 733s Read 1 reference strings 733s Checked 0 alignments, 0 edits 733s --------------- 733s /usr/bin/bowtie2 -i L,0.395108470033957 --mp 8.55125433898374,6.31853686323186 --cp-ival 1 --local --trim5 0 --mm --rdg 5.70095371575144,17.2611525623118 --score-min L,2.15272600668562,6.82371897344297 --np 5 --cp-min 2 --large-index -q -p 4 -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 733s PASSED 733s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 734s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read '5' because it was < 2 characters long 734s Warning: skipping mate #1 of read '10' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '10' because it was < 2 characters long 734s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '13' because it was < 2 characters long 734s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read '14' because it was < 2 characters long 734s Warning: skipping mate #2 of read '120' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read '120' because it was < 2 characters long 734s 124 reads; of these: 734s 124 (100.00%) were paired; of these: 734s 124 (100.00%) aligned concordantly 0 times 734s 0 (0.00%) aligned concordantly exactly 1 time 734s 0 (0.00%) aligned concordantly >1 times 734s ---- 734s 124 pairs aligned concordantly 0 times; of these: 734s 0 (0.00%) aligned discordantly 1 time 734s ---- 734s 124 pairs aligned 0 times concordantly or discordantly; of these: 734s 248 mates make up the pairs; of these: 734s 248 (100.00%) aligned 0 times 734s 0 (0.00%) aligned exactly 1 time 734s 0 (0.00%) aligned >1 times 734s 0.00% overall alignment rate 734s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 734s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 734s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 734s Flattened IUPAC characters 734s Mutating sequence Sim.pm.2 734s Introducing 5 SNPs, 1/0 ref/read gaps, and 2 rearrangements 734s Finished SNPs 734s Finished ref gaps 734s Finished read gaps 734s Mutating sequence Sim.pm.1 734s Introducing 15 SNPs, 0/1 ref/read gaps, and 0 rearrangements 734s Finished SNPs 734s Finished ref gaps 734s Finished read gaps 734s Mutated reference genome to subject genome 734s SNPs introduced: 20 734s Reference gaps introduced: 1 734s Read gaps introduced: 1 734s Rearrangements introduced: 2 734s Created read sampler 734s Sampling 117 reads 734s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.qseq & /tmp/Sim.pm.qtk7xXsv_2.qseq 734s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 734s *** Run 88 of 100 734s /usr/bin/bowtie2 -M 3 --large-index --cp-min 6 --np 2 --norc --cp-ival 5 --score-min L,7.66885916649039,3.60890504985905 --trim3 4 --rdg 45.4299163490268,12.0545556017371 --mm --qseq -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq 734s parsing sequence Sim.pm.1... 734s parsing sequence Sim.pm.2... 734s Parsed 40 reference bases 734s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 734s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 734s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 734s Read 50 alignments... 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 734s Warning: skipping mate #2 of read 'R_1_1_1_58_58_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 734s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 734s Read 100 alignments... 734s Read 150 alignments... 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 734s 117 reads; of these: 734s 110 (94.02%) were paired; of these: 734s 110 (100.00%) aligned concordantly 0 times 734s 0 (0.00%) aligned concordantly exactly 1 time 734s 0 (0.00%) aligned concordantly >1 times 734s ---- 734s 110 pairs aligned concordantly 0 times; of these: 734s 0 (0.00%) aligned discordantly 1 time 734s ---- 734s 110 pairs aligned 0 times concordantly or discordantly; of these: 734s 220 mates make up the pairs; of these: 734s 215 (97.73%) aligned 0 times 734s 3 (1.36%) aligned exactly 1 time 734s 2 (0.91%) aligned >1 times 734s 7 (5.98%) were unpaired; of these: 734s 7 (100.00%) aligned 0 times 734s 0 (0.00%) aligned exactly 1 time 734s 0 (0.00%) aligned >1 times 734s 2.20% overall alignment rate 734s Read 200 alignments... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s TT 734s TT 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s TG 734s TG 734s Processing line... 734s Processing line... 734s CTTCGCGAGGAG 734s CTTCGCGAGGAG 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s CTTCGCGAGGA 734s CTTCGCGAGGA 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s CG 734s CG 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s --- Summary --- 734s Read 1 reference strings 734s Checked 5 alignments, 0 edits 734s --------------- 734s PASSED 734s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 734s /usr/bin/bowtie2 -M 3 --large-index --cp-min 6 --np 2 --norc --cp-ival 5 --score-min L,7.66885916649039,3.60890504985905 --trim3 4 --rdg 45.4299163490268,12.0545556017371 --mm --qseq -p 3 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.qseq -2 /tmp/Sim.pm.qtk7xXsv_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 734s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 734s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 734s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 734s Warning: skipping mate #2 of read 'R_1_1_1_58_58_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 734s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 734s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 734s 117 reads; of these: 734s 110 (94.02%) were paired; of these: 734s 110 (100.00%) aligned concordantly 0 times 734s 0 (0.00%) aligned concordantly exactly 1 time 734s 0 (0.00%) aligned concordantly >1 times 734s ---- 734s 110 pairs aligned concordantly 0 times; of these: 734s 0 (0.00%) aligned discordantly 1 time 734s ---- 734s 110 pairs aligned 0 times concordantly or discordantly; of these: 734s 220 mates make up the pairs; of these: 734s 215 (97.73%) aligned 0 times 734s 3 (1.36%) aligned exactly 1 time 734s 2 (0.91%) aligned >1 times 734s 7 (5.98%) were unpaired; of these: 734s 7 (100.00%) aligned 0 times 734s 0 (0.00%) aligned exactly 1 time 734s 0 (0.00%) aligned >1 times 734s 2.20% overall alignment rate 734s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 734s Flattened IUPAC characters 734s Mutating sequence Sim.pm.2 734s *** Run 89 of 100 734s /usr/bin/bowtie2 --cp-ival 1 --large-index --cp-min 6 --trim5 3 --norc --score-min L,3.52600831338703,8.16672739953354 --nofw --trim3 8 -k 3 -D 39 -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta 734s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 734s Finished SNPs 734s Finished ref gaps 734s Finished read gaps 734s Mutating sequence Sim.pm.1 734s Introducing 14 SNPs, 2/0 ref/read gaps, and 0 rearrangements 734s Finished SNPs 734s Finished ref gaps 734s Finished read gaps 734s Mutated reference genome to subject genome 734s SNPs introduced: 17 734s Reference gaps introduced: 2 734s Read gaps introduced: 0 734s Rearrangements introduced: 0 734s Created read sampler 734s Sampling 19 reads 734s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 734s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 734s parsing sequence Sim.pm.1... 734s parsing sequence Sim.pm.2... 734s Parsed 40 reference bases 734s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 734s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '10' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 734s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '11' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 734s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '13' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 734s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '16' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 734s 19 reads; of these: 734s 19 (100.00%) were unpaired; of these: 734s 19 (100.00%) aligned 0 times 734s 0 (0.00%) aligned exactly 1 time 734s 0 (0.00%) aligned >1 times 734s 0.00% overall alignment rate 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s --- Summary --- 734s Read 1 reference strings 734s Checked 0 alignments, 0 edits 734s --------------- 734s PASSED 734s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 734s /usr/bin/bowtie2 --cp-ival 1 --large-index --cp-min 6 --trim5 3 --norc --score-min L,3.52600831338703,8.16672739953354 --nofw --trim3 8 -k 3 -D 39 -f -p 3 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 734s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 734s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '10' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 734s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '11' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 734s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '13' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 734s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '16' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 734s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 734s 19 reads; of these: 734s 19 (100.00%) were unpaired; of these: 734s 19 (100.00%) aligned 0 times 734s 0 (0.00%) aligned exactly 1 time 734s 0 (0.00%) aligned >1 times 734s 0.00% overall alignment rate 734s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 734s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 734s Flattened IUPAC characters 734s Mutating sequence Sim.pm.1 734s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 734s Finished SNPs 734s Finished ref gaps 734s Finished read gaps 734s Mutating sequence Sim.pm.2 734s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 734s Finished SNPs 734s Finished ref gaps 734s Finished read gaps 734s Mutated reference genome to subject genome 734s SNPs introduced: 6 734s Reference gaps introduced: 0 734s Read gaps introduced: 0 734s Rearrangements introduced: 0 734s Created read sampler 734s Sampling 190 reads 734s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.raw & /tmp/Sim.pm.qtk7xXsv_2.raw 734s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 734s parsing sequence Sim.pm.1... 734s parsing sequence Sim.pm.2... 734s Parsed 40 reference bases 734s *** Run 90 of 100 734s /usr/bin/bowtie2 --rdg 30.0774840310151,16.6942235864741 --mm --rfg 48.2027948877018,17.3749605933538 --ma 7.90477555054516 --nofw --score-min L,2.19729829987993,5.5071909376938 --mp 9.7189603327362,5.73311254443348 --gbar 7 --cp-ival 1 --cp-min 2 --large-index -r -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.raw -2 /tmp/Sim.pm.qtk7xXsv_2.raw 734s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 734s Warning: skipping mate #1 of read '6' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '6' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 734s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '9' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 734s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '32' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 734s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read '42' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 734s Warning: skipping mate #1 of read '71' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '71' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 734s Warning: skipping mate #1 of read '79' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '79' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 734s Read 50 alignments... 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 734s Warning: skipping mate #1 of read '88' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '88' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 734s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read '89' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 734s Warning: skipping mate #2 of read '90' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read '90' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 734s Warning: skipping mate #2 of read '107' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read '107' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 734s Warning: skipping mate #2 of read '114' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read '114' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 734s Warning: skipping mate #1 of read '148' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '148' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 734s Read 100 alignments... 734s Read 150 alignments... 734s Read 200 alignments... 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 734s Read 250 alignments... 734s Read 300 alignments... 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 734s Warning: skipping mate #1 of read '180' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '180' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 734s 190 reads; of these: 734s 190 (100.00%) were paired; of these: 734s 190 (100.00%) aligned concordantly 0 times 734s 0 (0.00%) aligned concordantly exactly 1 time 734s 0 (0.00%) aligned concordantly >1 times 734s ---- 734s 190 pairs aligned concordantly 0 times; of these: 734s 0 (0.00%) aligned discordantly 1 time 734s ---- 734s 190 pairs aligned 0 times concordantly or discordantly; of these: 734s 380 mates make up the pairs; of these: 734s 362 (95.26%) aligned 0 times 734s 10 (2.63%) aligned exactly 1 time 734s 8 (2.11%) aligned >1 times 734s 4.74% overall alignment rate 734s Read 350 alignments... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s TCG 734s TCG 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s AT 734s AT 734s Processing line... 734s Processing line... 734s CTG 734s CTG 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s GGA 734s GGA 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s GAG 734s GAG 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s GC 734s GC 734s Processing line... 734s TCGCGAGGAGGA 734s TCGCGAGGAGGA 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s GGG 734s GGG 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s GG 734s GG 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s CTTCGCGAG 734s CTTCGCGAG 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s CGGG 734s CGGG 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s CTTC 734s CTTC 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s ACGG 734s ACGG 734s Processing line... 734s Processing line... 734s GGG 734s GGG 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s GG 734s GG 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s GC 734s GC 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s ATC 734s ATC 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s GCGAGGA 734s GCGAGGA 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s --- Summary --- 734s Read 1 reference strings 734s Checked 18 alignments, 0 edits 734s --------------- 734s PASSED 734s Flattened IUPAC characters 734s Mutating sequence Sim.pm.2 734s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 734s Finished SNPs 734s Finished ref gaps 734s Finished read gaps 734s Mutating sequence Sim.pm.1 734s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 734s Finished SNPs 734s Finished ref gaps 734s Finished read gaps 734s Mutated reference genome to subject genome 734s SNPs introduced: 3 734s Reference gaps introduced: 0 734s Read gaps introduced: 0 734s Rearrangements introduced: 1 734s Created read sampler 734s Sampling 16 reads 734s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 734s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 734s parsing sequence Sim.pm.1... 734s parsing sequence Sim.pm.2... 734s Parsed 40 reference bases 734s *** Run 91 of 100 734s /usr/bin/bowtie2 --trim5 0 --trim3 6 --cp-min 2 --large-index --score-min L,6.02666246670592,7.69813410860552 --cp-ival 1 -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq 734s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 734s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '2' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 734s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '5' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 734s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '6' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 734s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '9' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 734s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '11' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 734s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '12' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 734s 16 reads; of these: 734s 15 (93.75%) were paired; of these: 734s 15 (100.00%) aligned concordantly 0 times 734s 0 (0.00%) aligned concordantly exactly 1 time 734s 0 (0.00%) aligned concordantly >1 times 734s ---- 734s 15 pairs aligned concordantly 0 times; of these: 734s 0 (0.00%) aligned discordantly 1 time 734s ---- 734s 15 pairs aligned 0 times concordantly or discordantly; of these: 734s 30 mates make up the pairs; of these: 734s 27 (90.00%) aligned 0 times 734s 2 (6.67%) aligned exactly 1 time 734s 1 (3.33%) aligned >1 times 734s 1 (6.25%) were unpaired; of these: 734s 1 (100.00%) aligned 0 times 734s 0 (0.00%) aligned exactly 1 time 734s 0 (0.00%) aligned >1 times 734s 9.68% overall alignment rate 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s CTGC 734s CTGC 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s GCCGG 734s GCCGG 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s GA 734s GA 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 734s --- Summary --- 734s Read 1 reference strings 734s Checked 3 alignments, 0 edits 734s --------------- 734s PASSED 734s Flattened IUPAC characters 734s Mutating sequence Sim.pm.2 734s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 734s Finished SNPs 734s Finished ref gaps 734s Finished read gaps 734s Mutating sequence Sim.pm.1 734s Introducing 1 SNPs, 2/0 ref/read gaps, and 4 rearrangements 734s Finished SNPs 734s Finished ref gaps 734s Finished read gaps 734s Mutated reference genome to subject genome 734s SNPs introduced: 9 734s Reference gaps introduced: 3 734s Read gaps introduced: 0 734s Rearrangements introduced: 4 734s Created read sampler 734s Sampling 122 reads 734s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 734s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 734s parsing sequence Sim.pm.1... 734s parsing sequence Sim.pm.2... 734s *** Run 92 of 100 734s /usr/bin/bowtie2 --np 6 --cp-min 4 --large-index --rdg 1.1898628655534 --ma 16.7682820802107 --score-min L,1.31388906793695,6.04119717772201 --gbar 2 --cp-ival 1 -a --trim5 9 --rfg 41.1144245684734 -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq 734s Parsed 40 reference bases 734s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 734s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '5' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 734s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '6' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 734s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '9' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 734s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '16' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 734s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '17' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 734s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '19' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 734s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '26' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 734s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '29' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 734s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '30' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 734s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '37' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 734s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '42' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 734s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '44' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 734s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '48' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 734s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '55' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 734s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '64' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 734s Read 50 alignments... 734s Read 100 alignments... 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 734s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '67' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 734s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '76' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 734s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '79' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 734s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '81' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 734s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '84' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 734s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '95' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 734s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '96' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 734s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '108' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 734s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '109' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 734s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '110' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 734s Read 150 alignments... 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 734s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 734s Warning: skipping read '118' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 734s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 734s Warning: skipping mate #1 of read '120' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 734s Warning: skipping mate #2 of read '121' because length (1) <= # seed mismatches (0) 734s Warning: skipping mate #2 of read '121' because it was < 2 characters long 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 734s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 734s Read 200 alignments... 734s 122 reads; of these: 734s 105 (86.07%) were paired; of these: 734s 105 (100.00%) aligned concordantly 0 times 734s 0 (0.00%) aligned concordantly exactly 1 time 734s 0 (0.00%) aligned concordantly >1 times 734s ---- 734s 105 pairs aligned concordantly 0 times; of these: 734s 0 (0.00%) aligned discordantly 1 time 734s ---- 734s 105 pairs aligned 0 times concordantly or discordantly; of these: 734s 210 mates make up the pairs; of these: 734s 203 (96.67%) aligned 0 times 734s 1 (0.48%) aligned exactly 1 time 734s 6 (2.86%) aligned >1 times 734s 17 (13.93%) were unpaired; of these: 734s 17 (100.00%) aligned 0 times 734s 0 (0.00%) aligned exactly 1 time 734s 0 (0.00%) aligned >1 times 734s 3.08% overall alignment rate 734s Read 250 alignments... 734s Processing line... 734s Processing line... 734s Processing line... 734s Processing line... 735s /usr/bin/bowtie2 --np 6 --cp-min 4 --large-index --rdg 1.1898628655534 --ma 16.7682820802107 --score-min L,1.31388906793695,6.04119717772201 --gbar 2 --cp-ival 1 -a --trim5 9 --rfg 41.1144245684734 -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s TGC 735s TGC 735s Processing line... 735s TGC 735s TGC 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s CG 735s CG 735s Processing line... 735s CG 735s CG 735s Processing line... 735s CG 735s CG 735s Processing line... 735s CG 735s CG 735s Processing line... 735s CG 735s CG 735s Processing line... 735s CG 735s CG 735s Processing line... 735s CG 735s CG 735s Processing line... 735s CG 735s CG 735s Processing line... 735s CG 735s CG 735s Processing line... 735s CG 735s CG 735s Processing line... 735s CG 735s CG 735s Processing line... 735s CG 735s CG 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s TCTTC 735s TCTTC 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s GG 735s GG 735s Processing line... 735s GG 735s GG 735s Processing line... 735s GG 735s GG 735s Processing line... 735s CC 735s CC 735s Processing line... 735s GG 735s GG 735s Processing line... 735s GG 735s GG 735s Processing line... 735s GG 735s GG 735s Processing line... 735s GG 735s GG 735s Processing line... 735s CC 735s CC 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s CGG 735s CGG 735s Processing line... 735s CGG 735s CGG 735s Processing line... 735s CCG 735s CCG 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s AG 735s AG 735s Processing line... 735s AG 735s AG 735s Processing line... 735s AG 735s AG 735s Processing line... 735s CT 735s CT 735s Processing line... 735s CT 735s CT 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s CCG 735s CCG 735s Processing line... 735s CGG 735s CGG 735s Processing line... 735s CGG 735s CGG 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s --- Summary --- 735s Read 1 reference strings 735s Checked 35 alignments, 0 edits 735s --------------- 735s PASSED 735s ALSO checking that bowtie2 and bowtie2-align match up 735s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 735s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '5' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 735s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '6' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 735s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '9' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 735s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '16' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 735s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '17' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 735s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '19' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 735s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '26' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 735s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '29' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 735s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '30' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 735s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '37' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 735s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '42' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 735s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '44' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 735s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '48' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 735s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '55' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 735s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '64' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 735s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '67' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 735s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '76' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 735s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '79' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 735s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '81' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 735s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '84' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 735s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '95' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 735s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '96' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 735s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '108' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 735s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '109' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 735s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '110' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 735s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '118' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 735s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '120' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 735s Warning: skipping mate #2 of read '121' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '121' because it was < 2 characters long 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 735s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 735s 122 reads; of these: 735s 105 (86.07%) were paired; of these: 735s 105 (100.00%) aligned concordantly 0 times 735s 0 (0.00%) aligned concordantly exactly 1 time 735s 0 (0.00%) aligned concordantly >1 times 735s ---- 735s 105 pairs aligned concordantly 0 times; of these: 735s 0 (0.00%) aligned discordantly 1 time 735s ---- 735s 105 pairs aligned 0 times concordantly or discordantly; of these: 735s 210 mates make up the pairs; of these: 735s 203 (96.67%) aligned 0 times 735s 1 (0.48%) aligned exactly 1 time 735s 6 (2.86%) aligned >1 times 735s 17 (13.93%) were unpaired; of these: 735s 17 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 3.08% overall alignment rate 735s Flattened IUPAC characters 735s Mutating sequence Sim.pm.2 735s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 735s Finished SNPs 735s Finished ref gaps 735s Finished read gaps 735s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 735s Mutating sequence Sim.pm.1 735s Introducing 11 SNPs, 0/0 ref/read gaps, and 4 rearrangements 735s Finished SNPs 735s Finished ref gaps 735s Finished read gaps 735s Mutated reference genome to subject genome 735s SNPs introduced: 17 735s Reference gaps introduced: 1 735s Read gaps introduced: 0 735s Rearrangements introduced: 4 735s Created read sampler 735s Sampling 70 reads 735s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 735s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 735s parsing sequence Sim.pm.1... 735s parsing sequence Sim.pm.2... 735s Parsed 40 reference bases 735s *** Run 93 of 100 735s /usr/bin/bowtie2 --norc -M 4 --cp-ival 1 --local -i S,0.979720003565867 --mp 8.815608368873,1.53052451465958 --large-index --np 5 --cp-min 5 -R 4 --score-min L,3.86114587969957,4.62550825214395 --mm -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 735s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 735s 70 reads; of these: 735s 70 (100.00%) were paired; of these: 735s 70 (100.00%) aligned concordantly 0 times 735s 0 (0.00%) aligned concordantly exactly 1 time 735s 0 (0.00%) aligned concordantly >1 times 735s ---- 735s 70 pairs aligned concordantly 0 times; of these: 735s 0 (0.00%) aligned discordantly 1 time 735s ---- 735s 70 pairs aligned 0 times concordantly or discordantly; of these: 735s 140 mates make up the pairs; of these: 735s 140 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 0.00% overall alignment rate 735s Read 50 alignments... 735s Read 100 alignments... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s --- Summary --- 735s Read 1 reference strings 735s Checked 0 alignments, 0 edits 735s --------------- 735s PASSED 735s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 735s /usr/bin/bowtie2 --norc -M 4 --cp-ival 1 --local -i S,0.979720003565867 --mp 8.815608368873,1.53052451465958 --large-index --np 5 --cp-min 5 -R 4 --score-min L,3.86114587969957,4.62550825214395 --mm -f -p 2 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 735s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 735s 70 reads; of these: 735s 70 (100.00%) were paired; of these: 735s 70 (100.00%) aligned concordantly 0 times 735s 0 (0.00%) aligned concordantly exactly 1 time 735s 0 (0.00%) aligned concordantly >1 times 735s ---- 735s 70 pairs aligned concordantly 0 times; of these: 735s 0 (0.00%) aligned discordantly 1 time 735s ---- 735s 70 pairs aligned 0 times concordantly or discordantly; of these: 735s 140 mates make up the pairs; of these: 735s 140 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 0.00% overall alignment rate 735s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 735s Flattened IUPAC characters 735s Mutating sequence Sim.pm.1 735s Introducing 10 SNPs, 1/1 ref/read gaps, and 3 rearrangements 735s Finished SNPs 735s Finished ref gaps 735s Finished read gaps 735s Mutating sequence Sim.pm.2 735s Introducing 0 SNPs, 3/0 ref/read gaps, and 0 rearrangements 735s Finished SNPs 735s Finished ref gaps 735s Finished read gaps 735s Mutated reference genome to subject genome 735s SNPs introduced: 10 735s Reference gaps introduced: 4 735s Read gaps introduced: 1 735s Rearrangements introduced: 3 735s Created read sampler 735s Sampling 165 reads 735s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 735s *** Run 94 of 100 735s /usr/bin/bowtie2 --cp-ival 4 --local --trim5 7 --large-index -a --cp-min 3 --np 3 -D 37 --score-min L,4.74597772602369,6.44670483887657 --trim3 5 -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 735s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 735s parsing sequence Sim.pm.1... 735s parsing sequence Sim.pm.2... 735s Parsed 40 reference bases 735s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '10' because it was < 2 characters long 735s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '11' because it was < 2 characters long 735s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '13' because it was < 2 characters long 735s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '24' because it was < 2 characters long 735s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '28' because it was < 2 characters long 735s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '30' because it was < 2 characters long 735s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '36' because it was < 2 characters long 735s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '38' because it was < 2 characters long 735s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '39' because it was < 2 characters long 735s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '44' because it was < 2 characters long 735s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '51' because it was < 2 characters long 735s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '64' because it was < 2 characters long 735s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '69' because it was < 2 characters long 735s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '70' because it was < 2 characters long 735s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '71' because it was < 2 characters long 735s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '79' because it was < 2 characters long 735s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '80' because it was < 2 characters long 735s Read 50 alignments... 735s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '81' because it was < 2 characters long 735s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '83' because it was < 2 characters long 735s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '87' because it was < 2 characters long 735s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '88' because it was < 2 characters long 735s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '91' because it was < 2 characters long 735s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '94' because it was < 2 characters long 735s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '106' because it was < 2 characters long 735s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '107' because it was < 2 characters long 735s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '108' because it was < 2 characters long 735s Warning: skipping mate #1 of read '111' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '111' because it was < 2 characters long 735s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '121' because it was < 2 characters long 735s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '122' because it was < 2 characters long 735s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '123' because it was < 2 characters long 735s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '124' because it was < 2 characters long 735s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '125' because it was < 2 characters long 735s Warning: skipping mate #1 of read '135' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '135' because it was < 2 characters long 735s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '136' because it was < 2 characters long 735s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '137' because it was < 2 characters long 735s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '138' because it was < 2 characters long 735s Warning: skipping mate #1 of read '142' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '142' because it was < 2 characters long 735s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '143' because it was < 2 characters long 735s Warning: skipping mate #1 of read '146' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '146' because it was < 2 characters long 735s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '147' because it was < 2 characters long 735s Read 100 alignments... 735s Read 150 alignments... 735s Read 200 alignments... 735s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '151' because it was < 2 characters long 735s Warning: skipping mate #1 of read '156' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '156' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '156' because it was < 2 characters long 735s Warning: skipping mate #2 of read '156' because it was < 2 characters long 735s Warning: skipping mate #1 of read '160' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '160' because it was < 2 characters long 735s 165 reads; of these: 735s 120 (72.73%) were paired; of these: 735s 120 (100.00%) aligned concordantly 0 times 735s 0 (0.00%) aligned concordantly exactly 1 time 735s 0 (0.00%) aligned concordantly >1 times 735s ---- 735s 120 pairs aligned concordantly 0 times; of these: 735s 0 (0.00%) aligned discordantly 1 time 735s ---- 735s 120 pairs aligned 0 times concordantly or discordantly; of these: 735s 240 mates make up the pairs; of these: 735s 240 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 45 (27.27%) were unpaired; of these: 735s 45 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 0.00% overall alignment rate 735s Read 250 alignments... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s 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Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s --- Summary --- 735s Read 1 reference strings 735s Checked 0 alignments, 0 edits 735s --------------- 735s PASSED 735s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 735s /usr/bin/bowtie2 --cp-ival 4 --local --trim5 7 --large-index -a --cp-min 3 --np 3 -D 37 --score-min L,4.74597772602369,6.44670483887657 --trim3 5 -f -p 3 -x /tmp/Sim.pm.qtk7xXsv --reorder -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 735s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '10' because it was < 2 characters long 735s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '11' because it was < 2 characters long 735s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '13' because it was < 2 characters long 735s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '24' because it was < 2 characters long 735s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '28' because it was < 2 characters long 735s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '30' because it was < 2 characters long 735s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '36' because it was < 2 characters long 735s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '38' because it was < 2 characters long 735s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '39' because it was < 2 characters long 735s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '44' because it was < 2 characters long 735s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '51' because it was < 2 characters long 735s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '64' because it was < 2 characters long 735s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '69' because it was < 2 characters long 735s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '70' because it was < 2 characters long 735s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '71' because it was < 2 characters long 735s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '79' because it was < 2 characters long 735s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '80' because it was < 2 characters long 735s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '81' because it was < 2 characters long 735s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '83' because it was < 2 characters long 735s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '87' because it was < 2 characters long 735s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '88' because it was < 2 characters long 735s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '91' because it was < 2 characters long 735s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '94' because it was < 2 characters long 735s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '106' because it was < 2 characters long 735s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '107' because it was < 2 characters long 735s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '108' because it was < 2 characters long 735s Warning: skipping mate #1 of read '111' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '111' because it was < 2 characters long 735s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '121' because it was < 2 characters long 735s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '122' because it was < 2 characters long 735s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '123' because it was < 2 characters long 735s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '124' because it was < 2 characters long 735s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '125' because it was < 2 characters long 735s Warning: skipping mate #1 of read '135' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '135' because it was < 2 characters long 735s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '136' because it was < 2 characters long 735s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '137' because it was < 2 characters long 735s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '138' because it was < 2 characters long 735s Warning: skipping mate #1 of read '142' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '142' because it was < 2 characters long 735s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '143' because it was < 2 characters long 735s Warning: skipping mate #1 of read '146' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '146' because it was < 2 characters long 735s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '147' because it was < 2 characters long 735s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '151' because it was < 2 characters long 735s Warning: skipping mate #1 of read '156' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '156' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '156' because it was < 2 characters long 735s Warning: skipping mate #2 of read '156' because it was < 2 characters long 735s Warning: skipping mate #1 of read '160' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '160' because it was < 2 characters long 735s 165 reads; of these: 735s 120 (72.73%) were paired; of these: 735s 120 (100.00%) aligned concordantly 0 times 735s 0 (0.00%) aligned concordantly exactly 1 time 735s 0 (0.00%) aligned concordantly >1 times 735s ---- 735s 120 pairs aligned concordantly 0 times; of these: 735s 0 (0.00%) aligned discordantly 1 time 735s ---- 735s 120 pairs aligned 0 times concordantly or discordantly; of these: 735s 240 mates make up the pairs; of these: 735s 240 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 45 (27.27%) were unpaired; of these: 735s 45 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 0.00% overall alignment rate 735s Flattened IUPAC characters 735s Mutating sequence Sim.pm.1 735s Introducing 9 SNPs, 3/2 ref/read gaps, and 4 rearrangements 735s Finished SNPs 735s Finished ref gaps 735s Finished read gaps 735s Mutating sequence Sim.pm.2 735s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 735s Finished SNPs 735s Finished ref gaps 735s Finished read gaps 735s Mutated reference genome to subject genome 735s SNPs introduced: 12 735s Reference gaps introduced: 3 735s Read gaps introduced: 3 735s Rearrangements introduced: 4 735s Created read sampler 735s Sampling 91 reads 735s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 735s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 735s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 735s parsing sequence Sim.pm.1... 735s parsing sequence Sim.pm.2... 735s Parsed 40 reference bases 735s *** Run 95 of 100 735s /usr/bin/bowtie2 --rdg 41.3178347884752 --score-min L,7.32599318339928,1.79782735268368 --large-index --cp-min 2 --np 7 --rfg 24.2622364593158,5.93791804962002 -i S,1.26333164394982,1.04411105148002 -N 0 -L23 --trim3 7 --nofw --cp-ival 2 --local --trim5 7 -M 2 -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 735s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 735s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '1' because it was < 2 characters long 735s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '5' because it was < 2 characters long 735s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '9' because it was < 2 characters long 735s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '10' because it was < 2 characters long 735s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '20' because it was < 2 characters long 735s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '28' because it was < 2 characters long 735s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '30' because it was < 2 characters long 735s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '35' because it was < 2 characters long 735s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '39' because it was < 2 characters long 735s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '46' because it was < 2 characters long 735s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '48' because it was < 2 characters long 735s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '50' because it was < 2 characters long 735s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '60' because it was < 2 characters long 735s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '62' because it was < 2 characters long 735s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '64' because it was < 2 characters long 735s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '65' because it was < 2 characters long 735s Warning: skipping mate #2 of read '67' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '67' because it was < 2 characters long 735s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '73' because it was < 2 characters long 735s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '75' because it was < 2 characters long 735s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '80' because it was < 2 characters long 735s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '87' because it was < 2 characters long 735s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '88' because it was < 2 characters long 735s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '89' because it was < 2 characters long 735s Read 50 alignments... 735s Read 100 alignments... 735s 91 reads; of these: 735s 67 (73.63%) were paired; of these: 735s 67 (100.00%) aligned concordantly 0 times 735s 0 (0.00%) aligned concordantly exactly 1 time 735s 0 (0.00%) aligned concordantly >1 times 735s ---- 735s 67 pairs aligned concordantly 0 times; of these: 735s 0 (0.00%) aligned discordantly 1 time 735s ---- 735s 67 pairs aligned 0 times concordantly or discordantly; of these: 735s 134 mates make up the pairs; of these: 735s 134 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 24 (26.37%) were unpaired; of these: 735s 24 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 0.00% overall alignment rate 735s Read 150 alignments... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s --- Summary --- 735s Read 1 reference strings 735s Checked 0 alignments, 0 edits 735s --------------- 735s PASSED 735s Flattened IUPAC characters 735s Mutating sequence Sim.pm.1 735s Introducing 18 SNPs, 0/1 ref/read gaps, and 1 rearrangements 735s Finished SNPs 735s Finished ref gaps 735s Finished read gaps 735s Mutating sequence Sim.pm.2 735s Introducing 4 SNPs, 2/0 ref/read gaps, and 2 rearrangements 735s Finished SNPs 735s Finished ref gaps 735s Finished read gaps 735s Mutated reference genome to subject genome 735s SNPs introduced: 22 735s Reference gaps introduced: 2 735s Read gaps introduced: 1 735s Rearrangements introduced: 3 735s Created read sampler 735s Sampling 48 reads 735s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 735s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 735s parsing sequence Sim.pm.1... 735s parsing sequence Sim.pm.2... 735s Parsed 40 reference bases 735s *** Run 96 of 100 735s /usr/bin/bowtie2 --cp-min 3 --large-index --score-min L,7.8674472978958,7.8394092271802 -k 2 --rdg 29.3514920556344,6.99276907899667 --mm --n-ceil 0.62797640980128,0.248026702824174 --trim5 4 --norc --local --cp-ival 2 --trim3 4 --mp 7.65711694529976,1.51760699972352 -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq 735s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '5' because it was < 2 characters long 735s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '9' because it was < 2 characters long 735s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '10' because it was < 2 characters long 735s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '18' because it was < 2 characters long 735s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '20' because it was < 2 characters long 735s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '23' because it was < 2 characters long 735s Warning: skipping mate #2 of read '23' because it was < 2 characters long 735s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '29' because it was < 2 characters long 735s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '30' because it was < 2 characters long 735s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '31' because it was < 2 characters long 735s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '41' because it was < 2 characters long 735s 48 reads; of these: 735s 39 (81.25%) were paired; of these: 735s 39 (100.00%) aligned concordantly 0 times 735s 0 (0.00%) aligned concordantly exactly 1 time 735s 0 (0.00%) aligned concordantly >1 times 735s ---- 735s 39 pairs aligned concordantly 0 times; of these: 735s 0 (0.00%) aligned discordantly 1 time 735s ---- 735s 39 pairs aligned 0 times concordantly or discordantly; of these: 735s 78 mates make up the pairs; of these: 735s 78 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 9 (18.75%) were unpaired; of these: 735s 9 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 0.00% overall alignment rate 735s Read 50 alignments... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s Processing line... 735s --- Summary --- 735s Read 1 reference strings 735s Checked 0 alignments, 0 edits 735s --------------- 735s PASSED 735s ALSO checking that bowtie2 and bowtie2-align match up 735s /usr/bin/bowtie2 --cp-min 3 --large-index --score-min L,7.8674472978958,7.8394092271802 -k 2 --rdg 29.3514920556344,6.99276907899667 --mm --n-ceil 0.62797640980128,0.248026702824174 --trim5 4 --norc --local --cp-ival 2 --trim3 4 --mp 7.65711694529976,1.51760699972352 -q -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.als 735s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '5' because it was < 2 characters long 735s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '9' because it was < 2 characters long 735s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '10' because it was < 2 characters long 735s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '18' because it was < 2 characters long 735s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '20' because it was < 2 characters long 735s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '23' because it was < 2 characters long 735s Warning: skipping mate #2 of read '23' because it was < 2 characters long 735s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '29' because it was < 2 characters long 735s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '30' because it was < 2 characters long 735s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '31' because it was < 2 characters long 735s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '41' because it was < 2 characters long 735s 48 reads; of these: 735s 39 (81.25%) were paired; of these: 735s 39 (100.00%) aligned concordantly 0 times 735s 0 (0.00%) aligned concordantly exactly 1 time 735s 0 (0.00%) aligned concordantly >1 times 735s ---- 735s 39 pairs aligned concordantly 0 times; of these: 735s 0 (0.00%) aligned discordantly 1 time 735s ---- 735s 39 pairs aligned 0 times concordantly or discordantly; of these: 735s 78 mates make up the pairs; of these: 735s 78 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 9 (18.75%) were unpaired; of these: 735s 9 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 0.00% overall alignment rate 735s diff -uw /tmp/Sim.pm.qtk7xXsv.als /tmp/Sim.pm.qtk7xXsv.debug.als 735s /usr/bin/bowtie2 --cp-min 3 --large-index --score-min L,7.8674472978958,7.8394092271802 -k 2 --rdg 29.3514920556344,6.99276907899667 --mm --n-ceil 0.62797640980128,0.248026702824174 --trim5 4 --norc --local --cp-ival 2 --trim3 4 --mp 7.65711694529976,1.51760699972352 -q -p 4 -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fastq -2 /tmp/Sim.pm.qtk7xXsv_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 735s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 735s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '5' because it was < 2 characters long 735s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '9' because it was < 2 characters long 735s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '10' because it was < 2 characters long 735s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '18' because it was < 2 characters long 735s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '20' because it was < 2 characters long 735s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '23' because it was < 2 characters long 735s Warning: skipping mate #2 of read '23' because it was < 2 characters long 735s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 735s Warning: skipping mate #1 of read '29' because it was < 2 characters long 735s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '30' because it was < 2 characters long 735s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 735s Warning: skipping mate #2 of read '31' because it was < 2 characters long 735s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 735s Warning: skipping read '41' because it was < 2 characters long 735s 48 reads; of these: 735s 39 (81.25%) were paired; of these: 735s 39 (100.00%) aligned concordantly 0 times 735s 0 (0.00%) aligned concordantly exactly 1 time 735s 0 (0.00%) aligned concordantly >1 times 735s ---- 735s 39 pairs aligned concordantly 0 times; of these: 735s 0 (0.00%) aligned discordantly 1 time 735s ---- 735s 39 pairs aligned 0 times concordantly or discordantly; of these: 735s 78 mates make up the pairs; of these: 735s 78 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 9 (18.75%) were unpaired; of these: 735s 9 (100.00%) aligned 0 times 735s 0 (0.00%) aligned exactly 1 time 735s 0 (0.00%) aligned >1 times 735s 0.00% overall alignment rate 735s Flattened IUPAC characters 735s Mutating sequence Sim.pm.2 735s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 735s Finished SNPs 735s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 735s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 735s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 735s Finished ref gaps 735s Finished read gaps 735s Mutating sequence Sim.pm.1 735s Introducing 4 SNPs, 2/0 ref/read gaps, and 0 rearrangements 735s Finished SNPs 735s Finished ref gaps 735s Finished read gaps 735s Mutated reference genome to subject genome 735s SNPs introduced: 9 735s Reference gaps introduced: 3 735s Read gaps introduced: 0 735s Rearrangements introduced: 0 735s Created read sampler 735s Sampling 217 reads 735s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 735s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 735s parsing sequence Sim.pm.1... 735s parsing sequence Sim.pm.2... 735s Parsed 40 reference bases 735s *** Run 97 of 100 735s /usr/bin/bowtie2 --score-min L,7.12155287821404,7.9123892162708 --trim3 8 --rdg 7.15281347138302 --mm --large-index -M 7 --cp-min 2 --cp-ival 2 -f -x /tmp/Sim.pm.qtk7xXsv -1 /tmp/Sim.pm.qtk7xXsv_1.fasta -2 /tmp/Sim.pm.qtk7xXsv_2.fasta 736s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 736s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '5' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 736s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '10' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 736s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '17' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 736s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '26' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 736s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '36' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 736s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '44' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 736s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '52' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 736s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '54' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 736s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '58' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 736s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '64' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 736s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '65' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 736s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '69' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 736s Read 50 alignments... 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 736s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '82' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 736s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '89' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 736s Warning: skipping mate #1 of read '90' because length (1) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '90' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 736s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '95' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 736s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '105' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 736s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '111' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 736s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '114' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 736s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '118' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 736s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '120' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 736s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '123' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 736s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '125' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 736s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '132' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 736s Warning: skipping mate #1 of read '140' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '140' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 736s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '145' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 736s Warning: skipping mate #2 of read '150' because length (1) <= # seed mismatches (0) 736s Warning: skipping mate #2 of read '150' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 736s Warning: skipping mate #1 of read '152' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '152' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 736s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '153' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 736s Read 100 alignments... 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 736s Read 150 alignments... 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 736s Warning: skipping mate #1 of read '161' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #2 of read '161' because length (1) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '161' because it was < 2 characters long 736s Warning: skipping mate #2 of read '161' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 736s Warning: skipping mate #1 of read '164' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '164' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 736s Warning: skipping mate #1 of read '170' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #2 of read '170' because length (1) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '170' because it was < 2 characters long 736s Warning: skipping mate #2 of read '170' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 736s Read 200 alignments... 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 736s Warning: skipping mate #1 of read '181' because length (1) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '181' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 736s Warning: skipping mate #1 of read '182' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '182' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 736s Warning: skipping mate #1 of read '187' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '187' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 736s Read 250 alignments... 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '196; setting to 0 instead 736s Warning: skipping read '196' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '196' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 736s Warning: skipping mate #1 of read '198' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '198' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '201; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '201; setting to 0 instead 736s Warning: skipping mate #1 of read '201' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '201' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '202; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '202; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '203; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '204; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '204; setting to 0 instead 736s Warning: skipping mate #1 of read '204' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '204' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '205; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '205; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '206; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '206; setting to 0 instead 736s Warning: skipping mate #1 of read '206' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '206' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '207; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '207; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '208; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '208; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '209; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '209; setting to 0 instead 736s Warning: skipping mate #1 of read '209' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '209' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '210; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '210; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '211; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '212; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '212; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '213; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '213; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '214; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '215; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '216; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '216; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '217; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '217; setting to 0 instead 736s Warning: skipping mate #1 of read '217' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '217' because it was < 2 characters long 736s 217 reads; of these: 736s 167 (76.96%) were paired; of these: 736s 167 (100.00%) aligned concordantly 0 times 736s 0 (0.00%) aligned concordantly exactly 1 time 736s 0 (0.00%) aligned concordantly >1 times 736s ---- 736s 167 pairs aligned concordantly 0 times; of these: 736s 0 (0.00%) aligned discordantly 1 time 736s ---- 736s 167 pairs aligned 0 times concordantly or discordantly; of these: 736s 334 mates make up the pairs; of these: 736s 317 (94.91%) aligned 0 times 736s 4 (1.20%) aligned exactly 1 time 736s 13 (3.89%) aligned >1 times 736s 50 (23.04%) were unpaired; of these: 736s 48 (96.00%) aligned 0 times 736s 1 (2.00%) aligned exactly 1 time 736s 1 (2.00%) aligned >1 times 736s 4.95% overall alignment rate 736s Read 300 alignments... 736s Read 350 alignments... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CT 736s CT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CA 736s CA 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GG 736s GG 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CAT 736s CAT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s TG 736s TG 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CAT 736s CAT 736s Processing line... 736s Processing line... 736s GAGGA 736s GAGGA 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GGG 736s GGG 736s Processing line... 736s Processing line... 736s CC 736s CC 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s AC 736s AC 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GAGG 736s GAGG 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CCT 736s CCT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CT 736s CT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GAGGAGGAG 736s GAGGAGGAG 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CTTCGC 736s CTTCGC 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CT 736s CT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CGG 736s CGG 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GA 736s GA 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s TTC 736s TTC 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s --- Summary --- 736s Read 1 reference strings 736s Checked 19 alignments, 0 edits 736s --------------- 736s PASSED 736s Flattened IUPAC characters 736s Mutating sequence Sim.pm.1 736s Introducing 11 SNPs, 2/0 ref/read gaps, and 2 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s Mutating sequence Sim.pm.2 736s Introducing 13 SNPs, 0/0 ref/read gaps, and 0 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s Mutated reference genome to subject genome 736s SNPs introduced: 24 736s Reference gaps introduced: 2 736s Read gaps introduced: 0 736s Rearrangements introduced: 2 736s Created read sampler 736s Sampling 149 reads 736s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fasta & /tmp/Sim.pm.qtk7xXsv_2.fasta 736s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 736s parsing sequence Sim.pm.1... 736s parsing sequence Sim.pm.2... 736s Parsed 40 reference bases 736s *** Run 98 of 100 736s /usr/bin/bowtie2 --rfg 47.2097283018878,4.20670572694856 --mm --score-min L,1.37069894443704,2.76738193315801 --ma 9.15589780791258 --nofw --mp 9.85565777948634,8.95039236116379 --cp-ival 1 --large-index --cp-min 9 --trim5 1 -f -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta 736s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 736s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 736s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '6' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 736s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '16' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 736s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '23' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 736s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '33' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 736s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '43' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 736s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '55' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 736s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '94' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 736s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '95' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 736s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '96' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 736s Warning: skipping read '100' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '100' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 736s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '102' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 736s Warning: skipping read '105' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '105' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 736s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '126' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 736s 149 reads; of these: 736s 149 (100.00%) were unpaired; of these: 736s 141 (94.63%) aligned 0 times 736s 4 (2.68%) aligned exactly 1 time 736s 4 (2.68%) aligned >1 times 736s 5.37% overall alignment rate 736s Read 50 alignments... 736s Read 100 alignments... 736s Read 150 alignments... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GA 736s GA 736s Processing line... 736s Processing line... 736s TCGC 736s TCGC 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GG 736s GG 736s Processing line... 736s CGC 736s CGC 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CAT 736s CAT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s TG 736s TG 736s Processing line... 736s Processing line... 736s AT 736s AT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GGC 736s GGC 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s --- Summary --- 736s Read 1 reference strings 736s Checked 8 alignments, 0 edits 736s --------------- 736s PASSED 736s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 736s /usr/bin/bowtie2 --rfg 47.2097283018878,4.20670572694856 --mm --score-min L,1.37069894443704,2.76738193315801 --ma 9.15589780791258 --nofw --mp 9.85565777948634,8.95039236116379 --cp-ival 1 --large-index --cp-min 9 --trim5 1 -f -p 2 -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als 736s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 736s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 736s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '6' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 736s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '16' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 736s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '23' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 736s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '33' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 736s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '43' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 736s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '55' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 736s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '94' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 736s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '95' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 736s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '96' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 736s Warning: skipping read '100' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '100' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 736s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '102' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 736s Warning: skipping read '105' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '105' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 736s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '126' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 736s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.px.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.als.sorted 736s 149 reads; of these: 736s 149 (100.00%) were unpaired; of these: 736s 141 (94.63%) aligned 0 times 736s 4 (2.68%) aligned exactly 1 time 736s 4 (2.68%) aligned >1 times 736s 5.37% overall alignment rate 736s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qtk7xXsv.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.debug.als.sorted 736s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als.sorted /tmp/Sim.pm.qtk7xXsv.px.als.sorted 736s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 736s /usr/bin/bowtie2 --rfg 47.2097283018878,4.20670572694856 --mm --score-min L,1.37069894443704,2.76738193315801 --ma 9.15589780791258 --nofw --mp 9.85565777948634,8.95039236116379 --cp-ival 1 --large-index --cp-min 9 --trim5 1 -f -p 4 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 736s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 736s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 736s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '6' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 736s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '16' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 736s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '23' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 736s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '33' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 736s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '43' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 736s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '55' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 736s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '94' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 736s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '95' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 736s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '96' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 736s Warning: skipping read '100' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '100' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 736s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '102' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 736s Warning: skipping read '105' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '105' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 736s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '126' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 736s 149 reads; of these: 736s 149 (100.00%) were unpaired; of these: 736s 141 (94.63%) aligned 0 times 736s 4 (2.68%) aligned exactly 1 time 736s 4 (2.68%) aligned >1 times 736s 5.37% overall alignment rate 736s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 736s Flattened IUPAC characters 736s Mutating sequence Sim.pm.2 736s Introducing 2 SNPs, 2/0 ref/read gaps, and 0 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s Mutating sequence Sim.pm.1 736s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s Mutated reference genome to subject genome 736s SNPs introduced: 12 736s Reference gaps introduced: 2 736s Read gaps introduced: 0 736s Rearrangements introduced: 1 736s Created read sampler 736s Sampling 111 reads 736s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 736s *** Run 99 of 100 736s /usr/bin/bowtie2 --mm --score-min L,8.47997823581013,4.68895616874158 --gbar 3 --local --cp-ival 3 --large-index --cp-min 2 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 736s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 736s parsing sequence Sim.pm.1... 736s parsing sequence Sim.pm.2... 736s Parsed 40 reference bases 736s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '3' because it was < 2 characters long 736s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '95' because it was < 2 characters long 736s 111 reads; of these: 736s 111 (100.00%) were unpaired; of these: 736s 111 (100.00%) aligned 0 times 736s 0 (0.00%) aligned exactly 1 time 736s 0 (0.00%) aligned >1 times 736s 0.00% overall alignment rate 736s Read 50 alignments... 736s Read 100 alignments... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s /usr/bin/bowtie2 --mm --score-min L,8.47997823581013,4.68895616874158 --gbar 3 --local --cp-ival 3 --large-index --cp-min 2 -q -p 3 -x /tmp/Sim.pm.qtk7xXsv --reorder /tmp/Sim.pm.qtk7xXsv_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qtk7xXsv.px.reord.als 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s --- Summary --- 736s Read 1 reference strings 736s Checked 0 alignments, 0 edits 736s --------------- 736s PASSED 736s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 736s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '3' because it was < 2 characters long 736s Warning: skipping read '95' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '95' because it was < 2 characters long 736s 111 reads; of these: 736s 111 (100.00%) were unpaired; of these: 736s 111 (100.00%) aligned 0 times 736s 0 (0.00%) aligned exactly 1 time 736s 0 (0.00%) aligned >1 times 736s 0.00% overall alignment rate 736s diff -uw /tmp/Sim.pm.qtk7xXsv.debug.als /tmp/Sim.pm.qtk7xXsv.px.reord.als 736s Flattened IUPAC characters 736s Mutating sequence Sim.pm.1 736s Introducing 8 SNPs, 2/0 ref/read gaps, and 0 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s Mutating sequence Sim.pm.2 736s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s Mutated reference genome to subject genome 736s SNPs introduced: 10 736s Reference gaps introduced: 2 736s Read gaps introduced: 0 736s Rearrangements introduced: 0 736s Created read sampler 736s Sampling 78 reads 736s Dumping reads to temporary files /tmp/Sim.pm.qtk7xXsv_1.fastq & /tmp/Sim.pm.qtk7xXsv_2.fastq 736s Parsing FASTA file /tmp/Sim.pm.qtk7xXsv.fa... 736s parsing sequence Sim.pm.1... 736s parsing sequence Sim.pm.2... 736s *** Run 100 of 100 736s /usr/bin/bowtie2 --rfg 17.3603735466636,9.72595611899452 --mm --score-min L,8.63310314473406,4.76479653269411 --ma 20.2659588272714 --gbar 1 -D 39 --mp 7.86088796387216,4.95929014614768 -N 1 -L20 --cp-ival 4 --large-index --cp-min 2 -q -x /tmp/Sim.pm.qtk7xXsv /tmp/Sim.pm.qtk7xXsv_1.fastq 736s Parsed 40 reference bases 736s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 736s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 736s Warning: skipping read '11' because length (1) <= # seed mismatches (1) 736s Warning: skipping read '11' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 736s Warning: skipping read '13' because length (1) <= # seed mismatches (1) 736s Warning: skipping read '13' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 736s Warning: skipping read '14' because length (1) <= # seed mismatches (1) 736s Warning: skipping read '14' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 736s Warning: skipping read '24' because length (1) <= # seed mismatches (1) 736s Warning: skipping read '24' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 736s Warning: skipping read '51' because length (1) <= # seed mismatches (1) 736s Warning: skipping read '51' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 736s Warning: skipping read '76' because length (1) <= # seed mismatches (1) 736s Warning: skipping read '76' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 736s 78 reads; of these: 736s 78 (100.00%) were unpaired; of these: 736s 76 (97.44%) aligned 0 times 736s 2 (2.56%) aligned exactly 1 time 736s 0 (0.00%) aligned >1 times 736s 2.56% overall alignment rate 736s Read 50 alignments... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s AGGAGGAG 736s AGGAGGAG 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CGCGAG 736s CGCGAG 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s --- Summary --- 736s Read 1 reference strings 736s Checked 2 alignments, 0 edits 736s --------------- 736s PASSED 736s Created DNA generator 736s N frac: 0.009 736s IUPAC frac: 0.010 736s AT/ACGT frac: 0.328 736s A/AT frac: 0.269 736s C/CG frac: 0.283 736s Generating 2 references 736s Generated reference 'Sim.pm.1' of untrimmed length 297, trimmed length 87 736s Generated reference 'Sim.pm.2' of untrimmed length 281, trimmed length 79 736s Wrote references to /tmp/Sim.pm.pBDT5Pxz.fa 736s A: 16 736s *** TEST CASE *** 736s C: 27 736s G: 83 736s R: 1 736s T: 39 736s Executing: /usr/bin/bowtie2-build --dcv 32 --threads 1 --large-index --bmaxdivn 3 /tmp/Sim.pm.pBDT5Pxz.fa /tmp/Sim.pm.pBDT5Pxz 736s Settings: 736s Output files: "/tmp/Sim.pm.pBDT5Pxz.*.bt2l" 736s Line rate: 7 (line is 128 bytes) 736s Lines per side: 1 (side is 128 bytes) 736s Offset rate: 4 (one in 16) 736s FTable chars: 10 736s Strings: unpacked 736s Max bucket size: default 736s Max bucket size, sqrt multiplier: default 736s Max bucket size, len divisor: 3 736s Difference-cover sample period: 32 736s Endianness: little 736s Actual local endianness: little 736s Sanity checking: disabled 736s Building a LARGE index 736s Assertions: disabled 736s Random seed: 0 736s Sizeofs: void*:8, int:4, long:8, size_t:8 736s Input files DNA, FASTA: 736s /tmp/Sim.pm.pBDT5Pxz.fa 736s Reading reference sizes 736s Time reading reference sizes: 00:00:00 736s Calculating joined length 736s Writing header 736s Reserving space for joined string 736s Joining reference sequences 736s Time to join reference sequences: 00:00:00 736s bmax according to bmaxDivN setting: 55 736s Using parameters --bmax 42 --dcv 32 736s Doing ahead-of-time memory usage test 736s Passed! Constructing with these parameters: --bmax 42 --dcv 32 736s Constructing suffix-array element generator 736s Building DifferenceCoverSample 736s Building sPrime 736s Building sPrimeOrder 736s V-Sorting samples 736s V-Sorting samples time: 00:00:00 736s Allocating rank array 736s Ranking v-sort output 736s Ranking v-sort output time: 00:00:00 736s Invoking Larsson-Sadakane on ranks 736s Invoking Larsson-Sadakane on ranks time: 00:00:00 736s Sanity-checking and returning 736s Building samples 736s Reserving space for 10 sample suffixes 736s Generating random suffixes 736s QSorting 10 sample offsets, eliminating duplicates 736s QSorting sample offsets, eliminating duplicates time: 00:00:00 736s Multikey QSorting 10 samples 736s (Using difference cover) 736s Multikey QSorting samples time: 00:00:00 736s Calculating bucket sizes 736s Splitting and merging 736s Splitting and merging time: 00:00:00 736s Avg bucket size: 26.6667 (target: 41) 736s Converting suffix-array elements to index image 736s Allocating ftab, absorbFtab 736s Entering Ebwt loop 736s Getting block 1 of 6 736s Reserving size (42) for bucket 1 736s Calculating Z arrays for bucket 1 736s Entering block accumulator loop for bucket 1: 736s bucket 1: 10% 736s bucket 1: 20% 736s bucket 1: 30% 736s bucket 1: 40% 736s bucket 1: 50% 736s bucket 1: 60% 736s bucket 1: 70% 736s bucket 1: 80% 736s bucket 1: 90% 736s bucket 1: 100% 736s Sorting block of length 16 for bucket 1 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 17 for bucket 1 736s Getting block 2 of 6 736s Reserving size (42) for bucket 2 736s Calculating Z arrays for bucket 2 736s Entering block accumulator loop for bucket 2: 736s bucket 2: 10% 736s bucket 2: 20% 736s bucket 2: 30% 736s bucket 2: 40% 736s bucket 2: 50% 736s bucket 2: 60% 736s bucket 2: 70% 736s bucket 2: 80% 736s bucket 2: 90% 736s bucket 2: 100% 736s Sorting block of length 36 for bucket 2 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 37 for bucket 2 736s Getting block 3 of 6 736s Reserving size (42) for bucket 3 736s Calculating Z arrays for bucket 3 736s Entering block accumulator loop for bucket 3: 736s bucket 3: 10% 736s bucket 3: 20% 736s bucket 3: 30% 736s bucket 3: 40% 736s bucket 3: 50% 736s bucket 3: 60% 736s bucket 3: 70% 736s bucket 3: 80% 736s bucket 3: 90% 736s bucket 3: 100% 736s Sorting block of length 30 for bucket 3 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 31 for bucket 3 736s Getting block 4 of 6 736s Reserving size (42) for bucket 4 736s Calculating Z arrays for bucket 4 736s Entering block accumulator loop for bucket 4: 736s bucket 4: 10% 736s bucket 4: 20% 736s bucket 4: 30% 736s bucket 4: 40% 736s bucket 4: 50% 736s bucket 4: 60% 736s bucket 4: 70% 736s bucket 4: 80% 736s bucket 4: 90% 736s bucket 4: 100% 736s Sorting block of length 36 for bucket 4 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 37 for bucket 4 736s Getting block 5 of 6 736s Reserving size (42) for bucket 5 736s Calculating Z arrays for bucket 5 736s Entering block accumulator loop for bucket 5: 736s bucket 5: 10% 736s bucket 5: 20% 736s bucket 5: 30% 736s bucket 5: 40% 736s bucket 5: 50% 736s bucket 5: 60% 736s bucket 5: 70% 736s bucket 5: 80% 736s bucket 5: 90% 736s bucket 5: 100% 736s Sorting block of length 30 for bucket 5 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 31 for bucket 5 736s Getting block 6 of 6 736s Reserving size (42) for bucket 6 736s Calculating Z arrays for bucket 6 736s Entering block accumulator loop for bucket 6: 736s bucket 6: 10% 736s bucket 6: 20% 736s bucket 6: 30% 736s bucket 6: 40% 736s bucket 6: 50% 736s bucket 6: 60% 736s bucket 6: 70% 736s bucket 6: 80% 736s bucket 6: 90% 736s bucket 6: 100% 736s Sorting block of length 12 for bucket 6 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 13 for bucket 6 736s Exited Ebwt loop 736s fchr[A]: 0 736s fchr[C]: 16 736s fchr[G]: 43 736s fchr[T]: 126 736s fchr[$]: 165 736s Exiting Ebwt::buildToDisk() 736s Returning from initFromVector 736s Wrote 8389107 bytes to primary EBWT file: /tmp/Sim.pm.pBDT5Pxz.1.bt2l.tmp 736s Wrote 92 bytes to secondary EBWT file: /tmp/Sim.pm.pBDT5Pxz.2.bt2l.tmp 736s Re-opening _in1 and _in2 as input streams 736s Returning from Ebwt constructor 736s Headers: 736s len: 165 736s bwtLen: 166 736s sz: 42 736s bwtSz: 42 736s lineRate: 7 736s offRate: 4 736s offMask: 0xfffffffffffffff0 736s ftabChars: 10 736s eftabLen: 20 736s eftabSz: 160 736s ftabLen: 1048577 736s ftabSz: 8388616 736s offsLen: 11 736s offsSz: 88 736s lineSz: 128 736s sideSz: 128 736s sideBwtSz: 96 736s sideBwtLen: 384 736s numSides: 1 736s numLines: 1 736s ebwtTotLen: 128 736s ebwtTotSz: 128 736s color: 0 736s reverse: 0 736s Total time for call to driver() for forward index: 00:00:00 736s Reading reference sizes 736s Time reading reference sizes: 00:00:00 736s Calculating joined length 736s Writing header 736s Reserving space for joined string 736s Joining reference sequences 736s Time to join reference sequences: 00:00:00 736s Time to reverse reference sequence: 00:00:00 736s bmax according to bmaxDivN setting: 55 736s Using parameters --bmax 42 --dcv 32 736s Doing ahead-of-time memory usage test 736s Passed! Constructing with these parameters: --bmax 42 --dcv 32 736s Constructing suffix-array element generator 736s Building DifferenceCoverSample 736s Building sPrime 736s Building sPrimeOrder 736s V-Sorting samples 736s V-Sorting samples time: 00:00:00 736s Allocating rank array 736s Ranking v-sort output 736s Ranking v-sort output time: 00:00:00 736s Invoking Larsson-Sadakane on ranks 736s Invoking Larsson-Sadakane on ranks time: 00:00:00 736s Sanity-checking and returning 736s Building samples 736s Reserving space for 10 sample suffixes 736s Generating random suffixes 736s QSorting 10 sample offsets, eliminating duplicates 736s QSorting sample offsets, eliminating duplicates time: 00:00:00 736s Multikey QSorting 10 samples 736s (Using difference cover) 736s Multikey QSorting samples time: 00:00:00 736s Calculating bucket sizes 736s Splitting and merging 736s Splitting and merging time: 00:00:00 736s Split 1, merged 7; iterating... 736s Splitting and merging 736s Splitting and merging time: 00:00:00 736s Split 1, merged 0; iterating... 736s Splitting and merging 736s Splitting and merging time: 00:00:00 736s Avg bucket size: 32.2 (target: 41) 736s Converting suffix-array elements to index image 736s Allocating ftab, absorbFtab 736s Entering Ebwt loop 736s Getting block 1 of 5 736s Reserving size (42) for bucket 1 736s Calculating Z arrays for bucket 1 736s Entering block accumulator loop for bucket 1: 736s bucket 1: 10% 736s bucket 1: 20% 736s bucket 1: 30% 736s bucket 1: 40% 736s bucket 1: 50% 736s bucket 1: 60% 736s bucket 1: 70% 736s bucket 1: 80% 736s bucket 1: 90% 736s bucket 1: 100% 736s Sorting block of length 36 for bucket 1 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 37 for bucket 1 736s Getting block 2 of 5 736s Reserving size (42) for bucket 2 736s Calculating Z arrays for bucket 2 736s Entering block accumulator loop for bucket 2: 736s bucket 2: 10% 736s bucket 2: 20% 736s bucket 2: 30% 736s bucket 2: 40% 736s bucket 2: 50% 736s bucket 2: 60% 736s bucket 2: 70% 736s bucket 2: 80% 736s bucket 2: 90% 736s bucket 2: 100% 736s Sorting block of length 34 for bucket 2 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 35 for bucket 2 736s Getting block 3 of 5 736s Reserving size (42) for bucket 3 736s Calculating Z arrays for bucket 3 736s Entering block accumulator loop for bucket 3: 736s bucket 3: 10% 736s bucket 3: 20% 736s bucket 3: 30% 736s bucket 3: 40% 736s bucket 3: 50% 736s bucket 3: 60% 736s bucket 3: 70% 736s bucket 3: 80% 736s bucket 3: 90% 736s bucket 3: 100% 736s Sorting block of length 25 for bucket 3 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 26 for bucket 3 736s Getting block 4 of 5 736s Reserving size (42) for bucket 4 736s Calculating Z arrays for bucket 4 736s Entering block accumulator loop for bucket 4: 736s bucket 4: 10% 736s bucket 4: 20% 736s bucket 4: 30% 736s bucket 4: 40% 736s bucket 4: 50% 736s bucket 4: 60% 736s bucket 4: 70% 736s bucket 4: 80% 736s bucket 4: 90% 736s bucket 4: 100% 736s Sorting block of length 30 for bucket 4 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 31 for bucket 4 736s Getting block 5 of 5 736s Reserving size (42) for bucket 5 736s Calculating Z arrays for bucket 5 736s Entering block accumulator loop for bucket 5: 736s bucket 5: 10% 736s bucket 5: 20% 736s bucket 5: 30% 736s bucket 5: 40% 736s bucket 5: 50% 736s bucket 5: 60% 736s bucket 5: 70% 736s bucket 5: 80% 736s bucket 5: 90% 736s bucket 5: 100% 736s Sorting block of length 36 for bucket 5 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 37 for bucket 5 736s Exited Ebwt loop 736s fchr[A]: 0 736s fchr[C]: 16 736s fchr[G]: 43 736s fchr[T]: 126 736s fchr[$]: 165 736s Exiting Ebwt::buildToDisk() 736s Returning from initFromVector 736s Wrote 8389107 bytes to primary EBWT file: /tmp/Sim.pm.pBDT5Pxz.rev.1.bt2l.tmp 736s Wrote 92 bytes to secondary EBWT file: /tmp/Sim.pm.pBDT5Pxz.rev.2.bt2l.tmp 736s Renaming /tmp/Sim.pm.pBDT5Pxz.3.bt2l.tmp to /tmp/Sim.pm.pBDT5Pxz.3.bt2l 736s Re-opening _in1 and _in2 as input streams 736s Returning from Ebwt constructor 736s Headers: 736s len: 165 736s bwtLen: 166 736s sz: 42 736s bwtSz: 42 736s lineRate: 7 736s offRate: 4 736s offMask: 0xfffffffffffffff0 736s ftabChars: 10 736s eftabLen: 20 736s eftabSz: 160 736s ftabLen: 1048577 736s ftabSz: 8388616 736s offsLen: 11 736s offsSz: 88 736s lineSz: 128 736s sideSz: 128 736s sideBwtSz: 96 736s sideBwtLen: 384 736s numSides: 1 736s numLines: 1 736s ebwtTotLen: 128 736s ebwtTotSz: 128 736s color: 0 736s reverse: 1 736s Total time for backward call to driver() for mirror index: 00:00:00 736s Renaming /tmp/Sim.pm.pBDT5Pxz.4.bt2l.tmp to /tmp/Sim.pm.pBDT5Pxz.4.bt2l 736s Renaming /tmp/Sim.pm.pBDT5Pxz.1.bt2l.tmp to /tmp/Sim.pm.pBDT5Pxz.1.bt2l 736s Renaming /tmp/Sim.pm.pBDT5Pxz.2.bt2l.tmp to /tmp/Sim.pm.pBDT5Pxz.2.bt2l 736s Renaming /tmp/Sim.pm.pBDT5Pxz.rev.1.bt2l.tmp to /tmp/Sim.pm.pBDT5Pxz.rev.1.bt2l 736s Renaming /tmp/Sim.pm.pBDT5Pxz.rev.2.bt2l.tmp to /tmp/Sim.pm.pBDT5Pxz.rev.2.bt2l 736s Built nucleotide index '/tmp/Sim.pm.pBDT5Pxz' 736s Flattened IUPAC characters 736s Mutating sequence Sim.pm.2 736s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 736s Finished SNPs 736s *** Run 1 of 100 736s /usr/bin/bowtie2 --mm -R 1 -k 2 --ma 33.7397702969054 --score-min L,2.22564549100579,9.00075793688392 --np 3 --cp-min 2 --large-index --rfg 25.3617356930615,5.24188588585719 --cp-ival 2 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 736s Finished ref gaps 736s Finished read gaps 736s Mutating sequence Sim.pm.1 736s Introducing 12 SNPs, 3/1 ref/read gaps, and 0 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s Mutated reference genome to subject genome 736s SNPs introduced: 12 736s Reference gaps introduced: 4 736s Read gaps introduced: 2 736s Rearrangements introduced: 0 736s Created read sampler 736s Sampling 69 reads 736s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 736s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 736s parsing sequence Sim.pm.1... 736s parsing sequence Sim.pm.2... 736s Parsed 166 reference bases 736s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 736s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 736s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '14' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 736s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '29' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 736s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '33' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 736s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '36' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 736s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '46' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 736s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '66' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 736s 69 reads; of these: 736s 69 (100.00%) were unpaired; of these: 736s 57 (82.61%) aligned 0 times 736s 4 (5.80%) aligned exactly 1 time 736s 8 (11.59%) aligned >1 times 736s 17.39% overall alignment rate 736s Read 50 alignments... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s AGTGGCGGTCTGAGGCCG 736s AGTGGCGGTCTGAGGCCG 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GGCGGTTGACTTTCG 736s GGCGGTTGACTTTCG 736s Processing line... 736s GGCGGTTGACTTTCG 736s GGCGGTTGACTTTCG 736s Processing line... 736s TCGGGAGTGGGCG 736s TCGGGAGTGGGCG 736s Processing line... 736s CTTTAGGAGGG 736s CTTTAGGAGGG 736s Processing line... 736s CTTTAGGAGGG 736s CTTTAGGAGGG 736s Processing line... 736s TTAGGAGGGATGGGCCGGGGCGGCGGTT 736s TTAGGAGGGATGGGCCGGGGCGGCGGTT 736s Processing line... 736s TTAGGAGGGATGGGCCGGGGCGGCGGTT 736s TTAGGAGGGATGGGCCGGGGCGGCGGTT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CG 736s CG 736s Processing line... 736s CG 736s CG 736s /usr/bin/bowtie2 --mm -R 1 -k 2 --ma 33.7397702969054 --score-min L,2.22564549100579,9.00075793688392 --np 3 --cp-min 2 --large-index --rfg 25.3617356930615,5.24188588585719 --cp-ival 2 -r -p 4 -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GGCCGGGGCGGCGGTTGCTTTA 736s GGCCGGGGCGGCGGTTGCTTTA 736s Processing line... 736s GGCCGGGGCGGCGGTTGCTTTA 736s GGCCGGGGCGGCGGTTGCTTTA 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GCCGGGGCGGCG 736s GCCGGGGCGGCG 736s Processing line... 736s GCCGGGGCGGCG 736s GCCGGGGCGGCG 736s Processing line... 736s TCGGGA 736s TCGGGA 736s Processing line... 736s Processing line... 736s Processing line... 736s GTCTGAGGCCGG 736s GTCTGAGGCCGG 736s Processing line... 736s GGCGGCGGTTGCTTTAGGAGGGAT 736s GGCGGCGGTTGCTTTAGGAGGGAT 736s Processing line... 736s GGCGGCGGTTGCTTTAGGAGGGAT 736s GGCGGCGGTTGCTTTAGGAGGGAT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GGGG 736s GGGG 736s Processing line... 736s GGGG 736s GGGG 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s --- Summary --- 736s Read 1 reference strings 736s Checked 20 alignments, 0 edits 736s --------------- 736s PASSED 736s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 737s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 737s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 737s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '14' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 737s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '29' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 737s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '33' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 737s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '36' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 737s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '46' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 737s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '66' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 737s 69 reads; of these: 737s 69 (100.00%) were unpaired; of these: 737s 57 (82.61%) aligned 0 times 737s 4 (5.80%) aligned exactly 1 time 737s 8 (11.59%) aligned >1 times 737s 17.39% overall alignment rate 737s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 737s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 737s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 737s Flattened IUPAC characters 737s *** Run 2 of 100 737s /usr/bin/bowtie2 --rfg 22.5150418029067 --cp-ival 1 --local --norc --trim5 5 -M 4 --mm --rdg 19.2496561707094,16.6890940072821 --gbar 2 --score-min L,5.78502974041157,1.39230472983136 --large-index --cp-min 2 --np 2 -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq 737s Mutating sequence Sim.pm.2 737s Introducing 0 SNPs, 2/0 ref/read gaps, and 1 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutating sequence Sim.pm.1 737s Introducing 20 SNPs, 0/0 ref/read gaps, and 2 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutated reference genome to subject genome 737s SNPs introduced: 20 737s Reference gaps introduced: 2 737s Read gaps introduced: 0 737s Rearrangements introduced: 3 737s Created read sampler 737s Sampling 51 reads 737s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 737s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 737s parsing sequence Sim.pm.1... 737s parsing sequence Sim.pm.2... 737s Parsed 166 reference bases 737s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 737s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '2' because it was < 2 characters long 737s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '3' because it was < 2 characters long 737s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '8' because it was < 2 characters long 737s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '17' because it was < 2 characters long 737s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '27' because it was < 2 characters long 737s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '36' because it was < 2 characters long 737s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '44' because it was < 2 characters long 737s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '46' because it was < 2 characters long 737s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '49' because it was < 2 characters long 737s 51 reads; of these: 737s 51 (100.00%) were unpaired; of these: 737s 49 (96.08%) aligned 0 times 737s 2 (3.92%) aligned exactly 1 time 737s 0 (0.00%) aligned >1 times 737s 3.92% overall alignment rate 737s Read 50 alignments... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GTCATTGTAGTGGCGGTCTGAGGCCGGGTGATCGG 737s GTCATTGTAGTGGCGGTCTGAGGCCGGNTGATCGG 737s Processing line... 737s /usr/bin/bowtie2 --rfg 22.5150418029067 --cp-ival 1 --local --norc --trim5 5 -M 4 --mm --rdg 19.2496561707094,16.6890940072821 --gbar 2 --score-min L,5.78502974041157,1.39230472983136 --large-index --cp-min 2 --np 2 -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s TGGGCCGGTGCGGCGGTTGCTTTAGGAGGGATGGGCAGGGGCGACGGTTGCTTTAGGAG 737s TGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s --- Summary --- 737s Read 1 reference strings 737s Checked 2 alignments, 0 edits 737s --------------- 737s PASSED 737s ALSO checking that bowtie2 and bowtie2-align match up 737s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 737s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '2' because it was < 2 characters long 737s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 737s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 737s *** Run 3 of 100 737s /usr/bin/bowtie2 --trim5 8 --n-ceil 1.21413096911327,0.878098852531241 --norc -a --cp-ival 2 -i C,1.03678661544195 --mp 3.2965763193597,2.9793340751172 --rfg 9.50958890249723,17.6611024384358 --cp-min 7 --large-index --gbar 3 --ma 16.0517420994109 --score-min L,7.46062143154108,6.26723136599859 --rdg 23.7606298079032 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 737s Warning: skipping read '3' because it was < 2 characters long 737s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '8' because it was < 2 characters long 737s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '17' because it was < 2 characters long 737s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '27' because it was < 2 characters long 737s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '36' because it was < 2 characters long 737s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '44' because it was < 2 characters long 737s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '46' because it was < 2 characters long 737s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '49' because it was < 2 characters long 737s 51 reads; of these: 737s 51 (100.00%) were unpaired; of these: 737s 49 (96.08%) aligned 0 times 737s 2 (3.92%) aligned exactly 1 time 737s 0 (0.00%) aligned >1 times 737s 3.92% overall alignment rate 737s Flattened IUPAC characters 737s Mutating sequence Sim.pm.2 737s Introducing 5 SNPs, 3/5 ref/read gaps, and 2 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutating sequence Sim.pm.1 737s Introducing 13 SNPs, 1/2 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutated reference genome to subject genome 737s SNPs introduced: 18 737s Reference gaps introduced: 4 737s Read gaps introduced: 7 737s Rearrangements introduced: 2 737s Created read sampler 737s Sampling 163 reads 737s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 737s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 737s parsing sequence Sim.pm.1... 737s parsing sequence Sim.pm.2... 737s Parsed 166 reference bases 737s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 737s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '3' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 737s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '4' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 737s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '8' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 737s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '9' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 737s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '11' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 737s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '15' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 737s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '16' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 737s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '17' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 737s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '20' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 737s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '29' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 737s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '32' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 737s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '36' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 737s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '41' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 737s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '43' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 737s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '45' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 737s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '46' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 737s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '48' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 737s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '49' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 737s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '53' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 737s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '61' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 737s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '62' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 737s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '63' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 737s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '64' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 737s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '71' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 737s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '81' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 737s Read 50 alignments... 737s Read 100 alignments... 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 737s Read 150 alignments... 737s Read 200 alignments... 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 737s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '98' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 737s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '102' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 737s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '106' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 737s Warning: skipping mate #1 of read '107' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '107' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 737s Warning: skipping mate #2 of read '110' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '110' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 737s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '115' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 737s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '116' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 737s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '122' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 737s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '128' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 737s Warning: skipping mate #2 of read '130' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '130' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 737s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '132' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 737s Warning: skipping mate #1 of read '135' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '135' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '135' because it was < 2 characters long 737s Warning: skipping mate #2 of read '135' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 737s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '144' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 737s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '151' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 737s Warning: skipping mate #1 of read '153' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '153' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 737s Read 250 alignments... 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 737s Read 300 alignments... 737s 163 reads; of these: 737s 132 (80.98%) were paired; of these: 737s 132 (100.00%) aligned concordantly 0 times 737s 0 (0.00%) aligned concordantly exactly 1 time 737s 0 (0.00%) aligned concordantly >1 times 737s ---- 737s 132 pairs aligned concordantly 0 times; of these: 737s 0 (0.00%) aligned discordantly 1 time 737s ---- 737s 132 pairs aligned 0 times concordantly or discordantly; of these: 737s 264 mates make up the pairs; of these: 737s 252 (95.45%) aligned 0 times 737s 3 (1.14%) aligned exactly 1 time 737s 9 (3.41%) aligned >1 times 737s 31 (19.02%) were unpaired; of these: 737s 30 (96.77%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 1 (3.23%) aligned >1 times 737s 4.41% overall alignment rate 737s Read 350 alignments... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GGGCCG 737s GGGCCG 737s Processing line... 737s GGGCCG 737s GGGCCG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s TA 737s TA 737s Processing line... 737s TA 737s TA 737s Processing line... 737s TA 737s TA 737s Processing line... 737s TA 737s TA 737s Processing line... 737s CA 737s CA 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GTTGCTTTAGG 737s GTTGCTTTAGG 737s Processing line... 737s GTTGCTTTAGG 737s GTTGCTTTAGG 737s Processing line... 737s GTTGCTTTAGG 737s GTTGCTTTAGG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GGGCCGGGGCGGCGGTTG 737s GGGCCGGGGCGGCGGTTG 737s Processing line... 737s GGGCCGGGGCGGCGGTTG 737s GGGCCGGGGCGGCGGTTG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GCC 737s GCC 737s Processing line... 737s GCC 737s GCC 737s Processing line... 737s GCC 737s GCC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GTGGCGGT 737s GTGGCGGT 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CC 737s CC 737s Processing line... 737s CC 737s CC 737s Processing line... 737s CC 737s CC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s AGTGGGCGGTTGAC 737s AGTGGGCGGTTGAC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s --- Summary --- 737s Read 1 reference strings 737s Checked 111 alignments, 0 edits 737s --------------- 737s PASSED 737s Flattened IUPAC characters 737s Mutating sequence Sim.pm.1 737s Introducing 0 SNPs, 2/0 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutating sequence Sim.pm.2 737s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutated reference genome to subject genome 737s SNPs introduced: 8 737s Reference gaps introduced: 2 737s Read gaps introduced: 1 737s Rearrangements introduced: 0 737s Created read sampler 737s Sampling 49 reads 737s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 737s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 737s parsing sequence Sim.pm.1... 737s parsing sequence Sim.pm.2... 737s Parsed 166 reference bases 737s *** Run 4 of 100 737s /usr/bin/bowtie2 --cp-ival 1 --cp-min 8 --np 1 -M 4 --large-index --ma 17.8710000021546 --nofw --score-min L,3.3779336186705,7.35704210929041 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 737s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 737s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 737s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '12' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 737s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '22' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 737s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '24' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 737s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '43' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 737s 49 reads; of these: 737s 49 (100.00%) were paired; of these: 737s 48 (97.96%) aligned concordantly 0 times 737s 0 (0.00%) aligned concordantly exactly 1 time 737s 1 (2.04%) aligned concordantly >1 times 737s ---- 737s 48 pairs aligned concordantly 0 times; of these: 737s 0 (0.00%) aligned discordantly 1 time 737s ---- 737s 48 pairs aligned 0 times concordantly or discordantly; of these: 737s 96 mates make up the pairs; of these: 737s 90 (93.75%) aligned 0 times 737s 1 (1.04%) aligned exactly 1 time 737s 5 (5.21%) aligned >1 times 737s 8.16% overall alignment rate 737s Read 50 alignments... 737s Read 100 alignments... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGG 737s GGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GGAGGGATG 737s GGAGGGATG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CGGGAGTGGGCGG 737s CGGGAGTGGGCGG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CC 737s CC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GGG 737s GGG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s TTGCT 737s TTGCT 737s Processing line... 737s TTTAGGAGGGATGGGCCGGGGCGGCGGTT 737s TTTAGGAGGGATGGGCCGGGGCGGCGGTT 737s Processing line... 737s CC 737s CC 737s Processing line... 737s Processing line... 737s Processing line... 737s --- Summary --- 737s Read 1 reference strings 737s Checked 8 alignments, 0 edits 737s --------------- 737s PASSED 737s Flattened IUPAC characters 737s Mutating sequence Sim.pm.2 737s Introducing 12 SNPs, 2/0 ref/read gaps, and 1 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutating sequence Sim.pm.1 737s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutated reference genome to subject genome 737s SNPs introduced: 15 737s Reference gaps introduced: 2 737s Read gaps introduced: 1 737s Rearrangements introduced: 1 737s Created read sampler 737s Sampling 149 reads 737s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 737s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 737s *** Run 5 of 100 737s /usr/bin/bowtie2 --local --cp-ival 1 --large-index --cp-min 2 --n-ceil 0.185093840925478,1.20360906436423 --score-min L,5.97951056727134,4.55591615301225 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 737s parsing sequence Sim.pm.1... 737s parsing sequence Sim.pm.2... 737s Parsed 166 reference bases 737s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '3' because it was < 2 characters long 737s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '22' because it was < 2 characters long 737s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '52' because it was < 2 characters long 737s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '53' because it was < 2 characters long 737s Warning: skipping read '73' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '73' because it was < 2 characters long 737s Warning: skipping read '118' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '118' because it was < 2 characters long 737s Warning: skipping read '123' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '123' because it was < 2 characters long 737s Read 50 alignments... 737s Warning: skipping read '145' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '145' because it was < 2 characters long 737s Read 100 alignments... 737s 149 reads; of these: 737s 149 (100.00%) were unpaired; of these: 737s 149 (100.00%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 0 (0.00%) aligned >1 times 737s 0.00% overall alignment rate 737s Read 150 alignments... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s --- Summary --- 737s Read 1 reference strings 737s Checked 0 alignments, 0 edits 737s --------------- 737s PASSED 737s Flattened IUPAC characters 737s Mutating sequence Sim.pm.1 737s Introducing 10 SNPs, 0/4 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutating sequence Sim.pm.2 737s Introducing 6 SNPs, 1/2 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutated reference genome to subject genome 737s SNPs introduced: 16 737s Reference gaps introduced: 1 737s Read gaps introduced: 6 737s Rearrangements introduced: 0 737s Created read sampler 737s Sampling 78 reads 737s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 737s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 737s parsing sequence Sim.pm.1... 737s parsing sequence Sim.pm.2... 737s Parsed 166 reference bases 737s *** Run 6 of 100 737s /usr/bin/bowtie2 --cp-ival 3 --local --trim5 0 -M 6 --rfg 49.6444783549666,3.71820649367178 --trim3 8 --cp-min 15 --np 5 --large-index --mm --rdg 5.50907328970322,3.55042977714284 -D 19 --score-min L,2.48634145704053,4.21135259557747 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 737s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 737s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '18' because it was < 2 characters long 737s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '20' because it was < 2 characters long 737s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '23' because it was < 2 characters long 737s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '25' because it was < 2 characters long 737s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '32' because it was < 2 characters long 737s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '34' because it was < 2 characters long 737s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '35' because it was < 2 characters long 737s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '44' because it was < 2 characters long 737s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '50' because it was < 2 characters long 737s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '54' because it was < 2 characters long 737s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '57' because it was < 2 characters long 737s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '60' because it was < 2 characters long 737s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '64' because it was < 2 characters long 737s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '73' because it was < 2 characters long 737s 78 reads; of these: 737s 78 (100.00%) were unpaired; of these: 737s 78 (100.00%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 0 (0.00%) aligned >1 times 737s 0.00% overall alignment rate 737s Read 50 alignments... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s --- Summary --- 737s Read 1 reference strings 737s Checked 0 alignments, 0 edits 737s --------------- 737s PASSED 737s ALSO checking that bowtie2 and bowtie2-align match up 737s /usr/bin/bowtie2 --cp-ival 3 --local --trim5 0 -M 6 --rfg 49.6444783549666,3.71820649367178 --trim3 8 --cp-min 15 --np 5 --large-index --mm --rdg 5.50907328970322,3.55042977714284 -D 19 --score-min L,2.48634145704053,4.21135259557747 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 738s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 738s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '18' because it was < 2 characters long 738s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '20' because it was < 2 characters long 738s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '23' because it was < 2 characters long 738s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '25' because it was < 2 characters long 738s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '32' because it was < 2 characters long 738s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '34' because it was < 2 characters long 738s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '35' because it was < 2 characters long 738s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '44' because it was < 2 characters long 738s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '50' because it was < 2 characters long 738s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '54' because it was < 2 characters long 738s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '57' because it was < 2 characters long 738s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '60' because it was < 2 characters long 738s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '64' because it was < 2 characters long 738s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '73' because it was < 2 characters long 738s 78 reads; of these: 738s 78 (100.00%) were unpaired; of these: 738s 78 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 738s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 738s /usr/bin/bowtie2 --cp-ival 3 --local --trim5 0 -M 6 --rfg 49.6444783549666,3.71820649367178 --trim3 8 --cp-min 15 --np 5 --large-index --mm --rdg 5.50907328970322,3.55042977714284 -D 19 --score-min L,2.48634145704053,4.21135259557747 -r -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 738s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 738s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '18' because it was < 2 characters long 738s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '20' because it was < 2 characters long 738s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '23' because it was < 2 characters long 738s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '25' because it was < 2 characters long 738s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '32' because it was < 2 characters long 738s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '34' because it was < 2 characters long 738s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '35' because it was < 2 characters long 738s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '44' because it was < 2 characters long 738s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '50' because it was < 2 characters long 738s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '54' because it was < 2 characters long 738s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '57' because it was < 2 characters long 738s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '60' because it was < 2 characters long 738s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '64' because it was < 2 characters long 738s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '73' because it was < 2 characters long 738s 78 reads; of these: 738s 78 (100.00%) were unpaired; of these: 738s 78 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 738s Flattened IUPAC characters 738s Mutating sequence Sim.pm.2 738s Introducing 4 SNPs, 2/0 ref/read gaps, and 0 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutating sequence Sim.pm.1 738s Introducing 16 SNPs, 1/0 ref/read gaps, and 3 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutated reference genome to subject genome 738s SNPs introduced: 20 738s Reference gaps introduced: 3 738s Read gaps introduced: 0 738s Rearrangements introduced: 3 738s Created read sampler 738s Sampling 136 reads 738s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 738s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 738s parsing sequence Sim.pm.1... 738s parsing sequence Sim.pm.2... 738s Parsed 166 reference bases 738s *** Run 7 of 100 738s /usr/bin/bowtie2 --rdg 30.7437014585429 --mm --score-min L,8.09668176398517,1.71661858908487 --ma 7.52088768513662 -R 2 --large-index --cp-min 2 --np 5 --nofw --cp-ival 3 -a -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 738s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 738s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 738s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '12' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 738s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '34' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 738s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '47' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 738s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '60' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 738s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '99' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 738s Read 50 alignments... 738s Read 100 alignments... 738s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 738s Warning: skipping read '113' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '113' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 738s 136 reads; of these: 738s 136 (100.00%) were unpaired; of these: 738s 127 (93.38%) aligned 0 times 738s 4 (2.94%) aligned exactly 1 time 738s 5 (3.68%) aligned >1 times 738s 6.62% overall alignment rate 738s Read 150 alignments... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s CATTGTAGTGGCGGTCTGAGGCCG 738s CATTGTAGTGGCGGTCTGAGGCCG 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s GCGGTTGACTT 738s GCGGTTGACTT 738s Processing line... 738s GCGGTTGACTT 738s GCGGTTGACTT 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s GCG 738s GCG 738s Processing line... 738s GCG 738s GCG 738s Processing line... 738s GCG 738s GCG 738s Processing line... 738s GCG 738s GCG 738s Processing line... 738s GCG 738s GCG 738s Processing line... 738s GCG 738s GCG 738s Processing line... 738s /usr/bin/bowtie2 --rdg 30.7437014585429 --mm --score-min L,8.09668176398517,1.71661858908487 --ma 7.52088768513662 -R 2 --large-index --cp-min 2 --np 5 --nofw --cp-ival 3 -a -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 738s GCG 738s GCG 738s Processing line... 738s GCG 738s GCG 738s Processing line... 738s GCG 738s GCG 738s Processing line... 738s GCG 738s GCG 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s GCGGTTGACTT 738s GCGGTTGACTT 738s Processing line... 738s GCGGTTGACTT 738s GCGGTTGACTT 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s GCGGTTGACTTTCGGGTGTCATTGTAG 738s GCGGTTGACTTTCGGGTGTCATTGTAG 738s Processing line... 738s CCG 738s CCG 738s Processing line... 738s CCG 738s CCG 738s Processing line... 738s CCG 738s CCG 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s CA 738s CA 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s GACTTTCGGGTGTCATTGTAGTGGCGGTCTGAG 738s GACTTTCGGGTGTCATTGTAGTGGCGGTCTGAG 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s GCCG 738s GCCG 738s Processing line... 738s GCCG 738s GCCG 738s Processing line... 738s GCCG 738s GCCG 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s --- Summary --- 738s Read 1 reference strings 738s Checked 24 alignments, 0 edits 738s --------------- 738s PASSED 738s ALSO checking that bowtie2 and bowtie2-align match up 738s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 738s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 738s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '12' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 738s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '34' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 738s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '47' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 738s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '60' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 738s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '99' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 738s Warning: skipping read '113' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '113' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 738s 136 reads; of these: 738s 136 (100.00%) were unpaired; of these: 738s 127 (93.38%) aligned 0 times 738s 4 (2.94%) aligned exactly 1 time 738s 5 (3.68%) aligned >1 times 738s 6.62% overall alignment rate 738s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 738s /usr/bin/bowtie2 --rdg 30.7437014585429 --mm --score-min L,8.09668176398517,1.71661858908487 --ma 7.52088768513662 -R 2 --large-index --cp-min 2 --np 5 --nofw --cp-ival 3 -a -r -p 4 -x /tmp/Sim.pm.pBDT5Pxz --reorder /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 738s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 738s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 738s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 738s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '12' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 738s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '34' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 738s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '47' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 738s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '60' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 738s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '99' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 738s Warning: skipping read '113' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '113' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 738s 136 reads; of these: 738s 136 (100.00%) were unpaired; of these: 738s 127 (93.38%) aligned 0 times 738s 4 (2.94%) aligned exactly 1 time 738s 5 (3.68%) aligned >1 times 738s 6.62% overall alignment rate 738s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 738s Flattened IUPAC characters 738s Mutating sequence Sim.pm.1 738s Introducing 17 SNPs, 4/0 ref/read gaps, and 1 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutating sequence Sim.pm.2 738s Introducing 4 SNPs, 3/2 ref/read gaps, and 2 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutated reference genome to subject genome 738s SNPs introduced: 21 738s Reference gaps introduced: 7 738s Read gaps introduced: 2 738s Rearrangements introduced: 3 738s Created read sampler 738s Sampling 122 reads 738s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 738s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 738s parsing sequence Sim.pm.1... 738s parsing sequence Sim.pm.2... 738s Parsed 166 reference bases 738s *** Run 8 of 100 738s /usr/bin/bowtie2 --rdg 30.1774075809306 -D 42 -k 4 --score-min L,9.12509160238914,3.39850482152445 --large-index --np 3 --cp-min 4 -N 0 -L31 --mp 8.4734545751678,2.5119719139848 --trim3 2 --cp-ival 4 --local --trim5 2 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 738s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '11' because it was < 2 characters long 738s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '15' because it was < 2 characters long 738s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '16' because it was < 2 characters long 738s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '26' because it was < 2 characters long 738s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '34' because it was < 2 characters long 738s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '42' because it was < 2 characters long 738s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '45' because it was < 2 characters long 738s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '54' because it was < 2 characters long 738s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '56' because it was < 2 characters long 738s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '63' because it was < 2 characters long 738s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '64' because it was < 2 characters long 738s Read 50 alignments... 738s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '70' because it was < 2 characters long 738s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '78' because it was < 2 characters long 738s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '92' because it was < 2 characters long 738s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '100' because it was < 2 characters long 738s Warning: skipping mate #1 of read '103' because length (1) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '103' because it was < 2 characters long 738s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '104' because it was < 2 characters long 738s Read 100 alignments... 738s Read 150 alignments... 738s Read 200 alignments... 738s 122 reads; of these: 738s 114 (93.44%) were paired; of these: 738s 114 (100.00%) aligned concordantly 0 times 738s 0 (0.00%) aligned concordantly exactly 1 time 738s 0 (0.00%) aligned concordantly >1 times 738s ---- 738s 114 pairs aligned concordantly 0 times; of these: 738s 0 (0.00%) aligned discordantly 1 time 738s ---- 738s 114 pairs aligned 0 times concordantly or discordantly; of these: 738s 228 mates make up the pairs; of these: 738s 228 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 8 (6.56%) were unpaired; of these: 738s 8 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s /usr/bin/bowtie2 --rdg 30.1774075809306 -D 42 -k 4 --score-min L,9.12509160238914,3.39850482152445 --large-index --np 3 --cp-min 4 -N 0 -L31 --mp 8.4734545751678,2.5119719139848 --trim3 2 --cp-ival 4 --local --trim5 2 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s 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Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s --- Summary --- 738s Read 1 reference strings 738s Checked 0 alignments, 0 edits 738s --------------- 738s PASSED 738s ALSO checking that bowtie2 and bowtie2-align match up 739s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 739s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 739s Warning: skipping mate #1 of read '11' because it was < 2 characters long 739s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '15' because it was < 2 characters long 739s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '16' because it was < 2 characters long 739s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '26' because it was < 2 characters long 739s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '34' because it was < 2 characters long 739s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '42' because it was < 2 characters long 739s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '45' because it was < 2 characters long 739s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '54' because it was < 2 characters long 739s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '56' because it was < 2 characters long 739s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '63' because it was < 2 characters long 739s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '64' because it was < 2 characters long 739s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '70' because it was < 2 characters long 739s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '78' because it was < 2 characters long 739s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '92' because it was < 2 characters long 739s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '100' because it was < 2 characters long 739s Warning: skipping mate #1 of read '103' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '103' because it was < 2 characters long 739s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '104' because it was < 2 characters long 739s 122 reads; of these: 739s 114 (93.44%) were paired; of these: 739s 114 (100.00%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 0 (0.00%) aligned concordantly >1 times 739s ---- 739s 114 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 114 pairs aligned 0 times concordantly or discordantly; of these: 739s 228 mates make up the pairs; of these: 739s 228 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 8 (6.56%) were unpaired; of these: 739s 8 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.1 739s Introducing 11 SNPs, 1/1 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.2 739s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 16 739s Reference gaps introduced: 1 739s Read gaps introduced: 1 739s Rearrangements introduced: 1 739s Created read sampler 739s Sampling 43 reads 739s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 739s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 166 reference bases 739s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 739s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 739s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '13' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 739s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '20' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 739s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '21' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 739s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '25' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 739s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '32' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 739s 43 reads; of these: 739s 43 (100.00%) were paired; of these: 739s 43 (100.00%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 0 (0.00%) aligned concordantly >1 times 739s ---- 739s 43 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 43 pairs aligned 0 times concordantly or discordantly; of these: 739s 86 mates make up the pairs; of these: 739s 74 (86.05%) aligned 0 times 739s 4 (4.65%) aligned exactly 1 time 739s 8 (9.30%) aligned >1 times 739s 13.95% overall alignment rate 739s Read 50 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TGTAGT 739s TGTAGT 739s Processing line... 739s Processing line... 739s TGGGCGGTTGACTTTCGGGTGTCATTGTAGTGGCG 739s TGGGCGGTTGACTTTCGGGTGTCATTGTAGTGGCG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s AGGCCGG 739s AGGCCGG 739s Processing line... 739s Processing line... 739s GTGG 739s GTGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GGGCGG 739s GGGCGG 739s Processing line... 739s Processing line... 739s CG 739s CG 739s Processing line... 739s Processing line... 739s GCTT 739s GCTT 739s Processing line... 739s Processing line... 739s CCGGGGCG 739s CCGGGGCG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TCGGGAGTGGGCGG 739s TCGGGAGTGGGCGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GG 739s GG 739s Processing line... 739s Processing line... 739s CGGGGCG 739s CGGGGCG 739s Processing line... 739s Processing line... 739s CGGTTGCTTTAGGAGGGATGG 739s CGGTTGCTTTAGGAGGGATGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 12 alignments, 0 edits 739s --------------- 739s PASSED 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.2 739s Introducing 13 SNPs, 0/0 ref/read gaps, and 3 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.1 739s Introducing 12 SNPs, 1/1 ref/read gaps, and 2 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 25 739s Reference gaps introduced: 1 739s Read gaps introduced: 1 739s Rearrangements introduced: 5 739s Created read sampler 739s Sampling 38 reads 739s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 739s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 166 reference bases 739s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '2' because it was < 2 characters long 739s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '3' because it was < 2 characters long 739s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '5' because it was < 2 characters long 739s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '11' because it was < 2 characters long 739s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '22' because it was < 2 characters long 739s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '27' because it was < 2 characters long 739s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '28' because it was < 2 characters long 739s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '33' because it was < 2 characters long 739s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '36' because it was < 2 characters long 739s 38 reads; of these: 739s 38 (100.00%) were unpaired; of these: 739s 38 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 0 alignments, 0 edits 739s --------------- 739s PASSED 739s ALSO checking that bowtie2 and bowtie2-align match up 739s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '2' because it was < 2 characters long 739s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '3' because it was < 2 characters long 739s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '5' because it was < 2 characters long 739s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '11' because it was < 2 characters long 739s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '22' because it was < 2 characters long 739s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '27' because it was < 2 characters long 739s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '28' because it was < 2 characters long 739s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '33' because it was < 2 characters long 739s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '36' because it was < 2 characters long 739s 38 reads; of these: 739s 38 (100.00%) were unpaired; of these: 739s 38 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.1 739s Introducing 4 SNPs, 0/3 ref/read gaps, and 2 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.2 739s Introducing 13 SNPs, 1/0 ref/read gaps, and 2 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 17 739s Reference gaps introduced: 1 739s Read gaps introduced: 3 739s Rearrangements introduced: 4 739s Created read sampler 739s Sampling 79 reads 739s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 739s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 166 reference bases 739s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 739s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 739s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (1) 739s Warning: skipping mate #2 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 739s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (1) 739s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 739s Read 50 alignments... 739s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (1) 739s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 739s 79 reads; of these: 739s 69 (87.34%) were paired; of these: 739s 69 (100.00%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 0 (0.00%) aligned concordantly >1 times 739s ---- 739s 69 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 69 pairs aligned 0 times concordantly or discordantly; of these: 739s 138 mates make up the pairs; of these: 739s 127 (92.03%) aligned 0 times 739s 6 (4.35%) aligned exactly 1 time 739s 5 (3.62%) aligned >1 times 739s 10 (12.66%) were unpaired; of these: 739s 10 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 7.43% overall alignment rate 739s Read 100 alignments... 739s Read 150 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTT 739s CGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGC 739s GAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGC 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GGGATG 739s GGGATG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGC 739s CGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGC 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GGAGTGGGCGGTTGACTTTCGG 739s GGAGTGGGCGGTTGACTTTCGG 739s Processing line... 739s Processing line... 739s CGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTT 739s CGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TTTCGGGTGTGATTGTAGTGGCGGTTAGAGGCCGGGTGATCCGGAGTGGGCGGTTGACTT 739s TTTCGGGTGTCATTGTAGTGGCGGTCTGAGGCCGGNTGATCGGGAGTGGGCGGTTGACTT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGAAGG 739s TTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATG--GG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GAGTGGGCGG 739s GAGTGGGCGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GCTTTAGGA 739s GCTTTAGGA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGC--TTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGG 739s CGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGA-G 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 11 alignments, 0 edits 739s --------------- 739s PASSED 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.2 739s Introducing 6 SNPs, 0/0 ref/read gaps, and 2 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.1 739s Introducing 8 SNPs, 1/0 ref/read gaps, and 2 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 14 739s Reference gaps introduced: 1 739s Read gaps introduced: 0 739s Rearrangements introduced: 4 739s Created read sampler 739s Sampling 102 reads 739s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 739s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 166 reference bases 739s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 739s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '1' because it was < 2 characters long 739s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '9' because it was < 2 characters long 739s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '17' because it was < 2 characters long 739s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (1) 739s Warning: skipping mate #2 of read '25' because it was < 2 characters long 739s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '30' because it was < 2 characters long 739s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '33' because it was < 2 characters long 739s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '34' because it was < 2 characters long 739s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '36' because it was < 2 characters long 739s Warning: skipping mate #2 of read '36' because it was < 2 characters long 739s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '48' because it was < 2 characters long 739s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '55' because it was < 2 characters long 739s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '65' because it was < 2 characters long 739s Read 50 alignments... 739s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '66' because it was < 2 characters long 739s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '70' because it was < 2 characters long 739s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '78' because it was < 2 characters long 739s Warning: skipping mate #2 of read '94' because length (1) <= # seed mismatches (1) 739s Warning: skipping mate #2 of read '94' because it was < 2 characters long 739s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '97' because it was < 2 characters long 739s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '101' because it was < 2 characters long 739s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '102' because it was < 2 characters long 739s 102 reads; of these: 739s 92 (90.20%) were paired; of these: 739s 92 (100.00%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 0 (0.00%) aligned concordantly >1 times 739s ---- 739s 92 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 92 pairs aligned 0 times concordantly or discordantly; of these: 739s 184 mates make up the pairs; of these: 739s 184 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 10 (9.80%) were unpaired; of these: 739s 10 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s Read 100 alignments... 739s Read 150 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 0 alignments, 0 edits 739s --------------- 739s PASSED 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.2 739s Introducing 13 SNPs, 1/3 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.1 739s Introducing 11 SNPs, 5/3 ref/read gaps, and 3 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 24 739s Reference gaps introduced: 6 739s Read gaps introduced: 6 739s Rearrangements introduced: 3 739s Created read sampler 739s Sampling 82 reads 739s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 739s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 166 reference bases 739s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 739s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 739s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 739s Read 50 alignments... 739s 82 reads; of these: 739s 64 (78.05%) were paired; of these: 739s 64 (100.00%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 0 (0.00%) aligned concordantly >1 times 739s ---- 739s 64 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 64 pairs aligned 0 times concordantly or discordantly; of these: 739s 128 mates make up the pairs; of these: 739s 128 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 18 (21.95%) were unpaired; of these: 739s 18 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s Read 100 alignments... 739s Read 150 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 0 alignments, 0 edits 739s --------------- 739s PASSED 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.2 739s Introducing 16 SNPs, 0/1 ref/read gaps, and 2 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.1 739s Introducing 18 SNPs, 0/0 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 34 739s *** Run 9 of 100 739s /usr/bin/bowtie2 --score-min L,4.62617530917046,2.60291749483346 --ma 3.83541421266748 --rfg 26.8582110944893 -M 8 --large-index --cp-min 4 --n-ceil 0.697502513317258,0.971896068011953 --cp-ival 2 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 739s *** Run 10 of 100 739s /usr/bin/bowtie2 --mm --score-min L,3.26692505911395,8.76379989456525 --gbar 1 --large-index --np 1 --cp-min 11 --rfg 48.7836351569784,12.0411329611653 --nofw --trim3 5 -i L,0.278182977179789 --local --cp-ival 2 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 739s /usr/bin/bowtie2 --mm --score-min L,3.26692505911395,8.76379989456525 --gbar 1 --large-index --np 1 --cp-min 11 --rfg 48.7836351569784,12.0411329611653 --nofw --trim3 5 -i L,0.278182977179789 --local --cp-ival 2 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 739s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 739s *** Run 11 of 100 739s /usr/bin/bowtie2 --np 1 --cp-min 9 --large-index --mm --score-min L,4.34007597291211,1.20314494486308 --cp-ival 1 --local -M 4 -N 1 -L23 --trim3 9 --nofw --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 739s *** Run 12 of 100 739s /usr/bin/bowtie2 --local --cp-ival 3 --np 1 --cp-min 13 --large-index -M 3 --trim5 9 --score-min L,4.2073018143981,4.98820393718655 --mp 6.14204030720211,5.86368382136017 -N 1 -L28 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 739s *** Run 13 of 100 739s /usr/bin/bowtie2 --trim5 9 --local --cp-ival 1 --trim3 4 -N 0 -L26 --np 1 --cp-min 5 --large-index --score-min L,5.75723290926069,2.17054063197968 -D 19 -k 9 --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 739s *** Run 14 of 100 739s /usr/bin/bowtie2 --cp-min 9 --np 1 --large-index --score-min L,6.61092617685382,1.47472086052935 --mm --norc --trim5 3 --cp-ival 1 --local --trim3 8 --rfg 1.77636271807869,2.9261886653146 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta 739s /usr/bin/bowtie2 --cp-min 9 --np 1 --large-index --score-min L,6.61092617685382,1.47472086052935 --mm --norc --trim5 3 --cp-ival 1 --local --trim3 8 --rfg 1.77636271807869,2.9261886653146 -f -p 4 -x /tmp/Sim.pm.pBDT5Pxz --reorder /tmp/Sim.pm.pBDT5Pxz_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 739s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 739s *** Run 15 of 100 739s /usr/bin/bowtie2 --mm --score-min L,1.49576461414806,1.0588678643125 --large-index --cp-min 7 --np 13 --nofw --local --cp-ival 3 -M 2 --n-ceil 0.80199123298249,1.06538194187799 --norc -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 739s /usr/bin/bowtie2 --mm --score-min L,1.49576461414806,1.0588678643125 --large-index --cp-min 7 --np 13 --nofw --local --cp-ival 3 -M 2 --n-ceil 0.80199123298249,1.06538194187799 --norc -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 739s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 739s *** Run 16 of 100 739s /usr/bin/bowtie2 --score-min L,6.57502117421329,5.6892369341036 -R 4 --large-index --np 6 --cp-min 2 --nofw --mp 5.28381683450399,1.75769784972273 --trim5 7 --cp-ival 1 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 739s Reference gaps introduced: 0 739s Read gaps introduced: 1 739s Rearrangements introduced: 2 739s Created read sampler 739s Sampling 45 reads 739s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 739s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 166 reference bases 739s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '1' because it was < 2 characters long 739s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '2' because it was < 2 characters long 739s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '5' because it was < 2 characters long 739s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '6' because it was < 2 characters long 739s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '12' because it was < 2 characters long 739s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '14' because it was < 2 characters long 739s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '17' because it was < 2 characters long 739s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '27' because it was < 2 characters long 739s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '32' because it was < 2 characters long 739s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '35' because it was < 2 characters long 739s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '37' because it was < 2 characters long 739s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '40' because it was < 2 characters long 739s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '41' because it was < 2 characters long 739s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '43' because it was < 2 characters long 739s 45 reads; of these: 739s 45 (100.00%) were unpaired; of these: 739s 44 (97.78%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 1 (2.22%) aligned >1 times 739s 2.22% overall alignment rate 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GGGGCGGCGGTTGCT 739s GGGGCGGCGGTTGCT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 1 alignments, 0 edits 739s --------------- 739s PASSED 739s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 739s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '1' because it was < 2 characters long 739s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '2' because it was < 2 characters long 739s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '5' because it was < 2 characters long 739s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '6' because it was < 2 characters long 739s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '12' because it was < 2 characters long 739s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '14' because it was < 2 characters long 739s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '17' because it was < 2 characters long 739s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '27' because it was < 2 characters long 739s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '32' because it was < 2 characters long 739s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '35' because it was < 2 characters long 739s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '37' because it was < 2 characters long 739s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '40' because it was < 2 characters long 739s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '41' because it was < 2 characters long 739s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '43' because it was < 2 characters long 739s 45 reads; of these: 739s 45 (100.00%) were unpaired; of these: 739s 44 (97.78%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 1 (2.22%) aligned >1 times 739s 2.22% overall alignment rate 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.1 739s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.2 739s Introducing 1 SNPs, 3/3 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 11 739s Reference gaps introduced: 3 739s Read gaps introduced: 3 739s Rearrangements introduced: 0 739s Created read sampler 739s Sampling 79 reads 739s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 739s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 166 reference bases 739s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 739s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '66' because it was < 2 characters long 739s Warning: skipping mate #1 of read '78' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '78' because it was < 2 characters long 739s Read 50 alignments... 739s 79 reads; of these: 739s 79 (100.00%) were paired; of these: 739s 79 (100.00%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 0 (0.00%) aligned concordantly >1 times 739s ---- 739s 79 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 79 pairs aligned 0 times concordantly or discordantly; of these: 739s 158 mates make up the pairs; of these: 739s 158 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s Read 100 alignments... 739s Read 150 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 0 alignments, 0 edits 739s --------------- 739s PASSED 739s ALSO checking that bowtie2 and bowtie2-align match up 739s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 739s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '66' because it was < 2 characters long 739s Warning: skipping mate #1 of read '78' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '78' because it was < 2 characters long 739s 79 reads; of these: 739s 79 (100.00%) were paired; of these: 739s 79 (100.00%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 0 (0.00%) aligned concordantly >1 times 739s ---- 739s 79 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 79 pairs aligned 0 times concordantly or discordantly; of these: 739s 158 mates make up the pairs; of these: 739s 158 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.1 739s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.2 739s Introducing 11 SNPs, 0/0 ref/read gaps, and 1 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 17 739s Reference gaps introduced: 1 739s Read gaps introduced: 0 739s Rearrangements introduced: 1 739s Created read sampler 739s Sampling 159 reads 739s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 739s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 166 reference bases 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 739s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '0' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '0' because it was < 2 characters long 739s Warning: skipping mate #2 of read '0' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 739s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '4' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 739s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '27' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 739s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '30' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 739s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '39' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 739s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '46' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 739s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '48' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 739s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '49' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 739s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '56' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 739s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '59' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 739s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '62' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 739s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '77' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 739s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '87' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 739s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '93' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 739s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '97' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 739s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '99' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 739s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '103' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 739s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '107' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 739s Wa/usr/bin/bowtie2 --score-min L,6.57502117421329,5.6892369341036 -R 4 --large-index --np 6 --cp-min 2 --nofw --mp 5.28381683450399,1.75769784972273 --trim5 7 --cp-ival 1 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 739s rning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 739s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '126' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 739s Read 50 alignments... 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 739s Read 100 alignments... 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 739s Read 150 alignments... 739s Read 200 alignments... 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 739s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '129' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 739s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '132' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 739s Warning: skipping mate #1 of read '140' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '140' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 739s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '143' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 739s Warning: skipping mate #1 of read '146' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '146' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 739s Warning: skipping mate #1 of read '147' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '147' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 739s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '158' because it was < 2 characters long 739s 159 reads; of these: 739s 129 (81.13%) were paired; of these: 739s 126 (97.67%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 3 (2.33%) aligned concordantly >1 times 739s ---- 739s 126 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 126 pairs aligned 0 times concordantly or discordantly; of these: 739s 252 mates make up the pairs; of these: 739s 225 (89.29%) aligned 0 times 739s 7 (2.78%) aligned exactly 1 time 739s 20 (7.94%) aligned >1 times 739s 30 (18.87%) were unpaired; of these: 739s 25 (83.33%) aligned 0 times 739s 4 (13.33%) aligned exactly 1 time 739s 1 (3.33%) aligned >1 times 739s 13.19% overall alignment rate 739s Read 250 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GGCGGCGGTT 739s GGCGGCGGTT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GGGCGG 739s GGGCGG 739s Processing line... 739s TAGGAGGGATGGG 739s TAGGAGGGATGGG 739s Processing line... 739s TGGG 739s TGGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s AGTGG 739s AGTGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s ATCGGGAGTGGG 739s ATCGGGAGTGGG 739s Processing line... 739s TG 739s TG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CGGGGCGGCGGTTGCTTT 739s CGGGGCGGCGGTTGCTTT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GTGGC 739s GTGGC 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GGGCCGGGGCGGCG 739s GGGCCGGGGCGGCG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GGCGGTTGACTTTCGGGTGTCATTGTAGTGGCGGTCTGAGGC 739s GGCGGTTGACTTTCGGGTGTCATTGTAGTGGCGGTCTGAGGC 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CTTTCGGGTGT 739s CTTTCGGGTGT 739s Processing line... 739s Processing line... 739s GCTTTAGGAGGGA 739s GCTTTAGGAGGGA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TGG 739s TGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GAGGG 739s GAGGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GGGCGGCGGTTGCTTT 739s GGGCGGCGGTTGCTTT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CGGTTGCTTT 739s CGGTTGCTTT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TCGGGTGTCATTGTAGTGGCGGTCTGAGGCCGG 739s TCGGGTGTCATTGTAGTGGCGGTCTGAGGCCGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TA 739s TA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CTG 739s CTG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CA 739s CA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GCGGTTGA 739s GCGGTTGA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s ATG 739s ATG 739s Processing line... 739s Processing line... 739s Processing line... 739s GGGATGGGCCGG 739s GGGATGGGCCGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TCTG 739s TCTG 739s Processing line... 739s GGCGG 739s GGCGG 739s Processing line... 739s Processing line... 739s Processing line... 739s GGGCGG 739s GGGCGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GC 739s GC 739s Processing line... 739s Processing line... 739s GGTC 739s GGTC 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CC 739s CC 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GTGGGCGGTTGACTT 739s GTGGGCGGTTGACTT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TGGG 739s TGGG 739s Processing line... 739s Processing line... 739s GTCT 739s GTCT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GCGGTCT 739s GCGGTCT 739s Processing line... 739s AT 739s AT 739s Processing line... 739s CCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGG 739s CCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGG 739s Processing line... 739s Processing line... 739s GT 739s GT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GGC 739s GGC 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 38 alignments, 0 edits 739s --------------- 739s PASSED 739s ALSO checking that bowtie2 and bowtie2-align match up 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 739s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '0' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '0' because it was < 2 characters long 739s Warning: skipping mate #2 of read '0' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 739s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '4' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 739s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '27' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 739s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '30' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 739s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '39' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 739s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '46' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 739s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '48' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 739s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '49' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 739s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '56' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 739s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '59' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 739s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '62' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 739s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '77' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 739s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '87' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 739s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '93' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 739s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '97' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 739s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '99' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 739s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '103' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 739s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '107' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 739s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '126' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 739s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '129' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 739s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '132' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 739s Warning: skipping mate #1 of read '140' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '140' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 739s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '143' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 739s Warning: skipping mate #1 of read '146' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '146' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 739s Warning: skipping mate #1 of read '147' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '147' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 739s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '158' because it was < 2 characters long 739s 159 reads; of these: 739s 129 (81.13%) were paired; of these: 739s 126 (97.67%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 3 (2.33%) aligned concordantly >1 times 739s ---- 739s 126 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 126 pairs aligned 0 times concordantly or discordantly; of these: 739s 252 mates make up the pairs; of these: 739s 225 (89.29%) aligned 0 times 739s 7 (2.78%) aligned exactly 1 time 739s 20 (7.94%) aligned >1 times 739s 30 (18.87%) were unpaired; of these: 739s 25 (83.33%) aligned 0 times 739s 4 (13.33%) aligned exactly 1 time 739s 1 (3.33%) aligned >1 times 739s 13.19% overall alignment rate 739s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 739s /usr/bin/bowtie2 --score-min L,6.57502117421329,5.6892369341036 -R 4 --large-index --np 6 --cp-min 2 --nofw --mp 5.28381683450399,1.75769784972273 --trim5 7 --cp-ival 1 -r -p 2 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 739s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 739s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '0' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '0' because it was < 2 characters long 739s Warning: skipping mate #2 of read '0' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 739s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '4' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 739s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '27' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 739s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '30' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 739s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '39' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 739s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '46' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 739s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '48' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 739s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '49' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 739s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '56' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 739s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '59' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 739s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '62' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 739s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '87' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 739s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '93' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 739s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '97' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 739s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '99' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 739s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '103' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 739s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '107' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 739s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '126' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 739s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '129' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 739s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '132' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 739s Warning: skipping mate #1 of read '140' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '140' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 739s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '143' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 739s Warning: skipping mate #1 of read '146' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '146' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 739s Warning: skipping mate #1 of read '147' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '147' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 739s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '77' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 739s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '158' because it was < 2 characters long 739s 159 reads; of these: 739s 129 (81.13%) were paired; of these: 739s 126 (97.67%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 3 (2.33%) aligned concordantly >1 times 739s ---- 739s 126 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 126 pairs aligned 0 times concordantly or discordantly; of these: 739s 252 mates make up the pairs; of these: 739s 225 (89.29%) aligned 0 times 739s 7 (2.78%) aligned exactly 1 time 739s 20 (7.94%) aligned >1 times 739s 30 (18.87%) were unpaired; of these: 739s 25 (83.33%) aligned 0 times 739s 4 (13.33%) aligned exactly 1 time 739s 1 (3.33%) aligned >1 times 739s 13.19% overall alignment rate 739s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.2 739s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.1 739s Introducing 5 SNPs, 0/1 ref/read gaps, and 2 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 12 739s Reference gaps introduced: 0 739s Read gaps introduced: 1 739s Rearrangements introduced: 2 739s Created read sampler 739s Sampling 80 reads 739s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 739s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 166 reference bases 739s *** Run 17 of 100 739s /usr/bin/bowtie2 --large-index --np 1 --cp-min 2 -D 10 --gbar 2 -R 2 --score-min L,2.56484429073137,6.1104877965485 --mm --rdg 3.04205785299415 --trim5 7 --cp-ival 2 -N 1 -L18 --nofw -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 739s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 739s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '3' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 739s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '11' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 739s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '12' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 739s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '16' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 739s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '27' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 739s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '37' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 739s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '41' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 739s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '46' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 739s Warning: skipping read '48' because length (1) <= # seed mismatches (1) 739s Warning: skipping read '48' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 739s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '49' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 739s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '51' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 739s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '56' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 739s Warning: skipping read '58' because length (1) <= # seed mismatches (1) 739s Warning: skipping read '58' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 739s Warning: skipping read '60' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '60' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 739s Warning: skipping read '65' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '65' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 739s Warning: skipping read '69' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '69' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 739s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '77' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 739s Warning: skipping read '79' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '79' because it was < 2 characters long 739s 80 reads; of these: 739s 80 (100.00%) were unpaired; of these: 739s 71 (88.75%) aligned 0 times 739s 3 (3.75%) aligned exactly 1 time 739s 6 (7.50%) aligned >1 times 739s 11.25% overall alignment rate 739s Read 50 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s AG 739s AG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GGGTGTCATTGTAGTGGCGGT 739s GGGTGTCATTGTAGTGGCGGT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TCGGGTGTCATTGT 739s TCGGGTGTCATTGT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TAGGAGGGATGGGCCGGGGCGGCGG 739s TAGGAGGGATGGGCCGGGGCGGCGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CGGTTGCTTTAGGAGGGATG 739s CGGTTGCTTTAGGAGGGATG 739s Processing line... 739s Processing line... 739s CGG 739s CGG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CG 739s CG 739s Processing line... 739s GCGGCGGTTG 739s GCGGCGGTTG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CGGGA 739s CGGGA 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 9 alignments, 0 edits 739s --------------- 739s PASSED 739s ALSO checking that bowtie2 and bowtie2-align match up 739s /usr/bin/bowtie2 --large-index --np 1 --cp-min 2 -D 10 --gbar 2 -R 2 --score-min L,2.56484429073137,6.1104877965485 --mm --rdg 3.04205785299415 --trim5 7 --cp-ival 2 -N 1 -L18 --nofw -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 740s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 740s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '3' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 740s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '11' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 740s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '12' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 740s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '16' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 740s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '27' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 740s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '37' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 740s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '41' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 740s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '46' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 740s Warning: skipping read '48' because length (1) <= # seed mismatches (1) 740s Warning: skipping read '48' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 740s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '49' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 740s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '51' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 740s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '56' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 740s Warning: skipping read '58' because length (1) <= # seed mismatches (1) 740s Warning: skipping read '58' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 740s Warning: skipping read '60' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '60' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 740s Warning: skipping read '65' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '65' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 740s Warning: skipping read '69' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '69' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 740s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '77' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 740s Warning: skipping read '79' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '79' because it was < 2 characters long 740s 80 reads; of these: 740s 80 (100.00%) were unpaired; of these: 740s 71 (88.75%) aligned 0 times 740s 3 (3.75%) aligned exactly 1 time 740s 6 (7.50%) aligned >1 times 740s 11.25% overall alignment rate 740s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 740s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 740s /usr/bin/bowtie2 --large-index --np 1 --cp-min 2 -D 10 --gbar 2 -R 2 --score-min L,2.56484429073137,6.1104877965485 --mm --rdg 3.04205785299415 --trim5 7 --cp-ival 2 -N 1 -L18 --nofw -r -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 740s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 740s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '3' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 740s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '11' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 740s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '12' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 740s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '16' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 740s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '27' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 740s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '37' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 740s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '41' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 740s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '46' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 740s Warning: skipping read '48' because length (1) <= # seed mismatches (1) 740s Warning: skipping read '48' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 740s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '49' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 740s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '51' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 740s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '56' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 740s Warning: skipping read '58' because length (1) <= # seed mismatches (1) 740s Warning: skipping read '58' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 740s Warning: skipping read '60' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '60' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 740s Warning: skipping read '65' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '65' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 740s Warning: skipping read '69' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '69' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 740s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '77' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 740s Warning: skipping read '79' because length (0) <= # seed mismatches (1) 740s Warning: skipping read '79' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 740s 80 reads; of these: 740s 80 (100.00%) were unpaired; of these: 740s 71 (88.75%) aligned 0 times 740s 3 (3.75%) aligned exactly 1 time 740s 6 (7.50%) aligned >1 times 740s 11.25% overall alignment rate 740s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.1 740s Introducing 5 SNPs, 2/0 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.2 740s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 13 740s Reference gaps introduced: 2 740s Read gaps introduced: 1 740s Rearrangements introduced: 0 740s Created read sampler 740s Sampling 114 reads 740s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 740s *** Run 18 of 100 740s /usr/bin/bowtie2 --mm --score-min L,9.013999098069,9.11119498892295 --trim3 7 --mp 9.94644747369366,7.11120568236917 --cp-ival 1 --large-index --cp-min 3 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 740s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 166 reference bases 740s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 740s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '9' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 740s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '10' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 740s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '17' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 740s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '18' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 740s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '23' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 740s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '24' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 740s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read '30' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 740s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '32' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 740s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '37' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 740s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '54' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 740s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '59' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 740s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '67' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 740s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '71' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 740s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '80' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 740s Read 50 alignments... 740s Read 100 alignments... 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 740s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '110' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 740s Read 150 alignments... 740s Read 200 alignments... 740s 114 reads; of these: 740s 96 (84.21%) were paired; of these: 740s 95 (98.96%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 1 (1.04%) aligned concordantly >1 times 740s ---- 740s 95 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 95 pairs aligned 0 times concordantly or discordantly; of these: 740s 190 mates make up the pairs; of these: 740s 154 (81.05%) aligned 0 times 740s 7 (3.68%) aligned exactly 1 time 740s 29 (15.26%) aligned >1 times 740s 18 (15.79%) were unpaired; of these: 740s 14 (77.78%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 4 (22.22%) aligned >1 times 740s 20.00% overall alignment rate 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s AGGAGGGATGGGC 740s AGGAGGGATGGGC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCG 740s GCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCG 740s Processing line... 740s Processing line... 740s GGGCCGG 740s GGGCCGG 740s Processing line... 740s Processing line... 740s TCGGGAGT 740s TCGGGAGT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TTTAGGAGGGATG 740s TTTAGGAGGGATG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGCCGGGGCGGCGGTTGCTTTA 740s GGCCGGGGCGGCGGTTGCTTTA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CGGCGGTTGCT 740s CGGCGGTTGCT 740s Processing line... 740s Processing line... 740s ATGGGCCGG 740s ATGGGCCGG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CGGGGCGGCGGTTGCTTTAGGAGGGATGGGC 740s CGGGGCGGCGGTTGCTTTAGGAGGGATGGGC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGG 740s GGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGG 740s Processing line... 740s Processing line... 740s GTCTG 740s GTCTG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GTGGGC 740s GTGGGC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GCGGTTGACTTTCGGG 740s GCGGTTGACTTTCGGG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GTGG 740s GTGG 740s Processing line... 740s Processing line... 740s GTGGG 740s GTGGG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGA 740s GGA 740s Processing line... 740s GGAGGGATGGG 740s GGAGGGATGGG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TTGCTTTAGGAGGGATGGGCCGGGG 740s TTGCTTTAGGAGGGATGGGCCGGGG 740s Processing line... 740s CC 740s CC 740s Processing line... 740s GAC 740s GAC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGGGCGGCGGTTGCTTTAGGAGGGATGGGC 740s GGGGCGGCGGTTGCTTTAGGAGGGATGGGC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GCCGGGGCGG 740s GCCGGGGCGG 740s Processing line... 740s Processing line... 740s TAGGAGGGATGG 740s TAGGAGGGATGG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GCT 740s GCT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GCT 740s GCT 740s Processing line... 740s GGCCGGG 740s GGCCGGG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGGCGGCGGTT 740s GGGCGGCGGTT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GAC 740s GAC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGC 740s TTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGC 740s Processing line... 740s Processing line... 740s CTTTAGGAGGGATGGGCCGG 740s CTTTAGGAGGGATGGGCCGG 740s Processing line... 740s GGA 740s GGA 740s Processing line... 740s GGCCGGG 740s GGCCGGG 740s Processing line... 740s Processing line... 740s ATGGGCCGGGGCGG 740s ATGGGCCGGGGCGG 740s Processing line... 740s Processing line... 740s TAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGG 740s TAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGG 740s Processing line... 740s Processing line... 740s AGGAGG 740s AGGAGG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGCCGGGGCGGCGGTTGCTTTAGGAGGG 740s GGCCGGGGCGGCGGTTGCTTTAGGAGGG 740s Processing line... 740s Processing line... 740s GGTGTCATT 740s GGTGTCATT 740s Processing line... 740s Processing line... 740s GGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 740s GGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 740s Processing line... 740s Processing line... 740s GGGCGGCGGTTGCT 740s GGGCGGCGGTTGCT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGTTGCTTTAGGAGGGATGGGCCGG 740s GGTTGCTTTAGGAGGGATGGGCCGG 740s Processing line... 740s Processing line... 740s CTT 740s CTT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GG 740s GG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 42 alignments, 0 edits 740s --------------- 740s PASSED 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.2 740s Introducing 2 SNPs, 2/1 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.1 740s Introducing 17 SNPs, 0/0 ref/read gaps, and 1 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 19 740s Reference gaps introduced: 2 740s Read gaps introduced: 1 740s Rearrangements introduced: 1 740s Created read sampler 740s Sampling 43 reads 740s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 740s *** Run 19 of 100 740s /usr/bin/bowtie2 --rfg 3.15204260029067 -i C,1.01799320966444 --mp 9.76851882754085,3.26688086552772 --trim3 6 --cp-ival 1 --local --trim5 2 --n-ceil 0.666067209614307,0.305452312558632 -k 3 -R 4 --score-min L,3.51574282433751,9.92157577180022 --large-index --cp-min 2 --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 740s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 166 reference bases 740s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 740s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 740s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 740s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 740s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 740s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 740s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 740s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 740s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 740s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 740s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 740s Warning: skipping mate #2 of read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 740s 43 reads; of these: 740s 35 (81.40%) were paired; of these: 740s 35 (100.00%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 0 (0.00%) aligned concordantly >1 times 740s ---- 740s 35 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 35 pairs aligned 0 times concordantly or discordantly; of these: 740s 70 mates make up the pairs; of these: 740s 70 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 8 (18.60%) were unpaired; of these: 740s 8 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 0.00% overall alignment rate 740s Read 50 alignments... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 0 alignments, 0 edits 740s --------------- 740s PASSED 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.2 740s Introducing 13 SNPs, 1/0 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.1 740s Introducing 18 SNPs, 0/1 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 31 740s Reference gaps introduced: 1 740s Read gaps introduced: 1 740s Rearrangements introduced: 0 740s Created read sampler 740s Sampling 101 reads 740s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 740s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s *** Run 20 of 100 740s /usr/bin/bowtie2 --mm -R 3 --trim3 6 --score-min L,9.62126252511857,6.51686247341955 --cp-ival 3 --local --np 7 --cp-min 2 --large-index -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta 740s Parsed 166 reference bases 740s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '22' because it was < 2 characters long 740s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '24' because it was < 2 characters long 740s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '27' because it was < 2 characters long 740s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '36' because it was < 2 characters long 740s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '39' because it was < 2 characters long 740s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '42' because it was < 2 characters long 740s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '47' because it was < 2 characters long 740s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '52' because it was < 2 characters long 740s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '53' because it was < 2 characters long 740s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '57' because it was < 2 characters long 740s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '62' because it was < 2 characters long 740s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '63' because it was < 2 characters long 740s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '70' because it was < 2 characters long 740s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '74' because it was < 2 characters long 740s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '89' because it was < 2 characters long 740s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '96' because it was < 2 characters long 740s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '99' because it was < 2 characters long 740s 101 reads; of these: 740s 101 (100.00%) were unpaired; of these: 740s 101 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 0.00% overall alignment rate 740s Read 50 alignments... 740s Read 100 alignments... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 0 alignments, 0 edits 740s --------------- 740s PASSED 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.2 740s Introducing 5 SNPs, 1/2 ref/read gaps, and 1 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.1 740s Introducing 13 SNPs, 1/0 ref/read gaps, and 1 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 18 740s Reference gaps introduced: 2 740s Read gaps introduced: 2 740s Rearrangements introduced: 2 740s Created read sampler 740s Sampling 17 reads 740s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 740s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 740s parsing sequence Sim.pm.1... 740s *** Run 21 of 100 740s /usr/bin/bowtie2 --trim5 2 --norc --large-index -M 3 --cp-min 4 --cp-ival 2 -R 2 --mp 6.81501209515893,2.62629731429521 --score-min L,7.25211343049521,7.4879768171711 --rfg 44.7592830693066,19.8512403631375 --rdg 37.7896090224929,6.62575943869984 --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 740s parsing sequence Sim.pm.2... 740s Parsed 166 reference bases 740s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s 17 reads; of these: 740s 17 (100.00%) were paired; of these: 740s 17 (100.00%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 0 (0.00%) aligned concordantly >1 times 740s ---- 740s 17 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 17 pairs aligned 0 times concordantly or discordantly; of these: 740s 34 mates make up the pairs; of these: 740s 29 (85.29%) aligned 0 times 740s 4 (11.76%) aligned exactly 1 time 740s 1 (2.94%) aligned >1 times 740s 14.71% overall alignment rate 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GCGGTTGACTTTCGGGTGTC 740s GCGGTTGACTTTCGGGTGTC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CGGGAGTGGGCGGTTGACTTTCG 740s CGGGAGTGGGCGGTTGACTTTCG 740s Processing line... 740s Processing line... 740s TGG 740s TGG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CGGGAG 740s CGGGAG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s /usr/bin/bowtie2 --trim5 2 --norc --large-index -M 3 --cp-min 4 --cp-ival 2 -R 2 --mp 6.81501209515893,2.62629731429521 --score-min L,7.25211343049521,7.4879768171711 --rfg 44.7592830693066,19.8512403631375 --rdg 37.7896090224929,6.62575943869984 --qseq -p 2 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TGATCGGGAGTGG 740s TGATCGGGAGTGG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 5 alignments, 0 edits 740s --------------- 740s PASSED 740s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 740s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s 17 reads; of these: 740s 17 (100.00%) were paired; of these: 740s 17 (100.00%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 0 (0.00%) aligned concordantly >1 times 740s ---- 740s 17 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 17 pairs aligned 0 times concordantly or discordantly; of these: 740s 34 mates make up the pairs; of these: 740s 29 (85.29%) aligned 0 times 740s 4 (11.76%) aligned exactly 1 time 740s 1 (2.94%) aligned >1 times 740s 14.71% overall alignment rate 740s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.1 740s Introducing 21 SNPs, 1/1 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.2 740s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 30 740s Reference gaps introduced: 1 740s Read gaps introduced: 1 740s Rearrangements introduced: 0 740s Created read sampler 740s Sampling 195 reads 740s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 740s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s *** Run 22 of 100 740s /usr/bin/bowtie2 --large-index --cp-min 4 --n-ceil 1.14821696518848,1.39113075786555 --local --cp-ival 1 --score-min L,6.17153697161965,2.75756564708104 --trim3 0 -k 6 -i S,1.37134389093343 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 740s Parsed 166 reference bases 740s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '12' because it was < 2 characters long 740s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '18' because it was < 2 characters long 740s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '22' because it was < 2 characters long 740s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '57' because it was < 2 characters long 740s Warning: skipping read '104' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '104' because it was < 2 characters long 740s Warning: skipping read '108' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '108' because it was < 2 characters long 740s Read 50 alignments... 740s Warning: skipping read '166' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '166' because it was < 2 characters long 740s Warning: skipping read '169' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '169' because it was < 2 characters long 740s Warning: skipping read '171' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '171' because it was < 2 characters long 740s Read 100 alignments... 740s 195 reads; of these: 740s 195 (100.00%) were unpaired; of these: 740s 195 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 0.00% overall alignment rate 740s Read 150 alignments... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 0 alignments, 0 edits 740s --------------- 740s PASSED 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.1 740s Introducing 14 SNPs, 0/2 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.2 740s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 19 740s Reference gaps introduced: 0 740s Read gaps introduced: 3 740s Rearrangements introduced: 0 740s Created read sampler 740s Sampling 106 reads 740s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 740s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 166 reference bases 740s *** Run 23 of 100 740s /usr/bin/bowtie2 --np 1 --cp-min 4 --large-index --score-min L,3.277597016001,6.73175174333104 -a --n-ceil 1.40363278743289,0.402559621360883 --cp-ival 2 --trim3 9 --nofw --mp 3.52665070247152,2.40774789343522 -N 0 -L27 --rfg 3.14247505744471 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 740s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 740s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '4' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 740s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '7' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 740s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '8' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 740s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '14' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 740s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '15' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 740s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '18' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 740s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '19' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 740s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '23' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 740s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '27' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 740s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '28' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 740s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '34' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 740s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '36' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 740s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '37' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 740s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '49' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 740s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '51' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 740s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '53' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 740s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '55' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 740s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '56' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 740s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '59' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 740s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '65' because it was < 2 characters long 740s Read 50 alignments... 740s Read 100 alignments... 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 740s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '66' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 740s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '78' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 740s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '79' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 740s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '84' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 740s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '87' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 740s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '92' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 740s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '93' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 740s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '94' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 740s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '96' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 740s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '97' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 740s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '106' because it was < 2 characters long 740s 106 reads; of these: 740s 87 (82.08%) were paired; of these: 740s 87 (100.00%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 0 (0.00%) aligned concordantly >1 times 740s ---- 740s 87 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 87 pairs aligned 0 times concordantly or discordantly; of these: 740s 174 mates make up the pairs; of these: 740s 162 (93.10%) aligned 0 times 740s 3 (1.72%) aligned exactly 1 time 740s 9 (5.17%) aligned >1 times 740s 19 (17.92%) were unpaired; of these: 740s 18 (94.74%) aligned 0 times 740s 1 (5.26%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 6.74% overall alignment rate 740s Read 150 alignments... 740s Read 200 alignments... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TGCTT 740s TGCTT 740s Processing line... 740s TGCTT 740s TGCTT 740s Processing line... 740s TGCTT 740s TGCTT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGGGCGGCG 740s GGGGCGGCG 740s Processing line... 740s GGGGCGGCG 740s GGGGCGGCG 740s Processing line... 740s GGGGCGGCG 740s GGGGCGGCG 740s Processing line... 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGT 740s GGT 740s Processing line... 740s GGT 740s GGT 740s Processing line... 740s GGT 740s GGT 740s Processing line... 740s GGT 740s GGT 740s Processing line... 740s GGT 740s GGT 740s Processing line... 740s GGT 740s GGT 740s Processing line... 740s GGT 740s GGT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s ATCGGGAGTGGGCGGTTG 740s ATCGGGAGTGGGCGGTTG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GATGGGCC 740s GATGGGCC 740s Processing line... 740s GATGGGCC 740s GATGGGCC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GAGTGGGC 740s GAGTGGGC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CGGC 740s CGGC 740s Processing line... 740s CGGC 740s CGGC 740s Processing line... 740s CGGC 740s CGGC 740s Processing line... 740s CGGC 740s CGGC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGGC 740s GGGC 740s Processing line... 740s GGGC 740s GGGC 740s Processing line... 740s GGGC 740s GGGC 740s Processing line... 740s GGGC 740s GGGC 740s Processing line... 740s GGGC 740s GGGC 740s Processing line... 740s GGGC 740s GGGC 740s Processing line... 740s GGGC 740s GGGC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGCCGGGGCGGCGG 740s GGCCGGGGCGGCGG 740s Processing line... 740s GGCCGGGGCGGCGG 740s GGCCGGGGCGGCGG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CGGTC 740s CGGTC 740s Processing line... 740s GCGGCGGTT 740s GCGGCGGTT 740s Processing line... 740s GCGGCGGTT 740s GCGGCGGTT 740s Processing line... 740s GCGGCGGTT 740s GCGGCGGTT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 51 alignments, 0 edits 740s --------------- 740s PASSED 740s ALSO checking that bowtie2 and bowtie2-align match up 740s /usr/bin/bowtie2 --np 1 --cp-min 4 --large-index --score-min L,3.277597016001,6.73175174333104 -a --n-ceil 1.40363278743289,0.402559621360883 --cp-ival 2 --trim3 9 --nofw --mp 3.52665070247152,2.40774789343522 -N 0 -L27 --rfg 3.14247505744471 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 740s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 740s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '4' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 740s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '7' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 740s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '8' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 740s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '14' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 740s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '15' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 740s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '18' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 740s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '19' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 740s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '23' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 740s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '27' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 740s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '28' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 740s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '34' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 740s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '36' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 740s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '37' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 740s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '49' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 740s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '51' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 740s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '53' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 740s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '55' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 740s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '56' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 740s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '59' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 740s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '65' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 740s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '66' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 740s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '78' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 740s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '79' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 740s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '84' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 740s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '87' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 740s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '92' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 740s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '93' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 740s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '94' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 740s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '96' because it was < 2 characters long 740s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 740s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 740s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '97' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 740s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '106' because it was < 2 characters long 740s 106 reads; of these: 740s 87 (82.08%) were paired; of these: 740s 87 (100.00%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 0 (0.00%) aligned concordantly >1 times 740s ---- 740s 87 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 87 pairs aligned 0 times concordantly or discordantly; of these: 740s 174 mates make up the pairs; of these: 740s 162 (93.10%) aligned 0 times 740s 3 (1.72%) aligned exactly 1 time 740s 9 (5.17%) aligned >1 times 740s 19 (17.92%) were unpaired; of these: 740s 18 (94.74%) aligned 0 times 740s 1 (5.26%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 6.74% overall alignment rate 740s /usr/bin/bowtie2 --np 1 --cp-min 4 --large-index --score-min L,3.277597016001,6.73175174333104 -a --n-ceil 1.40363278743289,0.402559621360883 --cp-ival 2 --trim3 9 --nofw --mp 3.52665070247152,2.40774789343522 -N 0 -L27 --rfg 3.14247505744471 -f -p 3 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 740s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 741s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '1' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 741s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '4' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 741s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '7' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 741s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '8' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 741s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '14' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 741s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '15' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 741s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '18' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 741s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '19' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 741s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '23' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 741s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '27' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 741s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '28' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 741s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '34' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 741s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '36' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 741s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '37' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 741s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '49' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 741s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '51' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 741s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '53' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 741s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '55' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 741s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '56' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 741s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '59' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 741s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '65' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 741s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '66' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 741s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '78' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 741s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '79' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 741s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '84' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 741s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '87' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 741s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '92' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 741s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '93' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 741s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '94' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 741s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '96' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 741s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '97' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 741s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '106' because it was < 2 characters long 741s 106 reads; of these: 741s 87 (82.08%) were paired; of these: 741s 87 (100.00%) aligned concordantly 0 times 741s 0 (0.00%) aligned concordantly exactly 1 time 741s 0 (0.00%) aligned concordantly >1 times 741s ---- 741s 87 pairs aligned concordantly 0 times; of these: 741s 0 (0.00%) aligned discordantly 1 time 741s ---- 741s 87 pairs aligned 0 times concordantly or discordantly; of these: 741s 174 mates make up the pairs; of these: 741s 162 (93.10%) aligned 0 times 741s 3 (1.72%) aligned exactly 1 time 741s 9 (5.17%) aligned >1 times 741s 19 (17.92%) were unpaired; of these: 741s 18 (94.74%) aligned 0 times 741s 1 (5.26%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 6.74% overall alignment rate 741s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 741s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 741s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 741s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 741s /usr/bin/bowtie2 --np 1 --cp-min 4 --large-index --score-min L,3.277597016001,6.73175174333104 -a --n-ceil 1.40363278743289,0.402559621360883 --cp-ival 2 --trim3 9 --nofw --mp 3.52665070247152,2.40774789343522 -N 0 -L27 --rfg 3.14247505744471 -f -p 4 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 741s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '1' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 741s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '4' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 741s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '7' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 741s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '8' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 741s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '14' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 741s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '15' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 741s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '18' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 741s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '19' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 741s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '23' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 741s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '27' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 741s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '28' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 741s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '34' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 741s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '36' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 741s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '37' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 741s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '49' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 741s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '51' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 741s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '53' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 741s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '55' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 741s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '56' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 741s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '59' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 741s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '65' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 741s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '66' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 741s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '78' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 741s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '79' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 741s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '84' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 741s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '87' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 741s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '92' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 741s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '93' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 741s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '94' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 741s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '96' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 741s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '97' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 741s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '106' because it was < 2 characters long 741s 106 reads; of these: 741s 87 (82.08%) were paired; of these: 741s 87 (100.00%) aligned concordantly 0 times 741s 0 (0.00%) aligned concordantly exactly 1 time 741s 0 (0.00%) aligned concordantly >1 times 741s ---- 741s 87 pairs aligned concordantly 0 times; of these: 741s 0 (0.00%) aligned discordantly 1 time 741s ---- 741s 87 pairs aligned 0 times concordantly or discordantly; of these: 741s 174 mates make up the pairs; of these: 741s 162 (93.10%) aligned 0 times 741s 3 (1.72%) aligned exactly 1 time 741s 9 (5.17%) aligned >1 times 741s 19 (17.92%) were unpaired; of these: 741s 18 (94.74%) aligned 0 times 741s 1 (5.26%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 6.74% overall alignment rate 741s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 741s Flattened IUPAC characters 741s Mutating sequence Sim.pm.1 741s Introducing 16 SNPs, 0/0 ref/read gaps, and 2 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutating sequence Sim.pm.2 741s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutated reference genome to subject genome 741s SNPs introduced: 26 741s Reference gaps introduced: 0 741s Read gaps introduced: 0 741s Rearrangements introduced: 3 741s Created read sampler 741s Sampling 42 reads 741s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 741s *** Run 24 of 100 741s /usr/bin/bowtie2 --score-min L,4.43598703949661,8.25803263109772 --rfg 30.0871182006807 --mm --n-ceil 0.513677412486905,0.761213662197423 --trim5 7 --large-index -M 4 --cp-min 5 --cp-ival 1 --local --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 741s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 741s parsing sequence Sim.pm.1... 741s parsing sequence Sim.pm.2... 741s Parsed 166 reference bases 741s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 741s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 741s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 741s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 741s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 741s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 741s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 741s *** Run 25 of 100 741s /usr/bin/bowtie2 -i C,1.11675136486248 -k 2 --trim3 6 --score-min L,5.02126235319641,5.34090439508524 --mm --rfg 4.69761667414448,17.8676291088334 --norc --cp-min 4 --large-index --cp-ival 1 --local -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 741s 42 reads; of these: 741s 37 (88.10%) were paired; of these: 741s 37 (100.00%) aligned concordantly 0 times 741s 0 (0.00%) aligned concordantly exactly 1 time 741s 0 (0.00%) aligned concordantly >1 times 741s ---- 741s 37 pairs aligned concordantly 0 times; of these: 741s 0 (0.00%) aligned discordantly 1 time 741s ---- 741s 37 pairs aligned 0 times concordantly or discordantly; of these: 741s 74 mates make up the pairs; of these: 741s 74 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 5 (11.90%) were unpaired; of these: 741s 5 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s Read 50 alignments... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s --- Summary --- 741s Read 1 reference strings 741s Checked 0 alignments, 0 edits 741s --------------- 741s PASSED 741s Flattened IUPAC characters 741s Mutating sequence Sim.pm.2 741s Introducing 10 SNPs, 1/3 ref/read gaps, and 0 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutating sequence Sim.pm.1 741s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutated reference genome to subject genome 741s SNPs introduced: 15 741s Reference gaps introduced: 1 741s Read gaps introduced: 3 741s Rearrangements introduced: 1 741s Created read sampler 741s Sampling 81 reads 741s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 741s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 741s parsing sequence Sim.pm.1... 741s parsing sequence Sim.pm.2... 741s Parsed 166 reference bases 741s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '8' because it was < 2 characters long 741s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '10' because it was < 2 characters long 741s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '19' because it was < 2 characters long 741s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '23' because it was < 2 characters long 741s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '26' because it was < 2 characters long 741s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '34' because it was < 2 characters long 741s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '43' because it was < 2 characters long 741s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '53' because it was < 2 characters long 741s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '61' because it was < 2 characters long 741s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '66' because it was < 2 characters long 741s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '67' because it was < 2 characters long 741s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '75' because it was < 2 characters long 741s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '78' because it was < 2 characters long 741s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '80' because it was < 2 characters long 741s 81 reads; of these: 741s 81 (100.00%) were unpaired; of these: 741s 81 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s Read 50 alignments... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s --- Summary --- 741s Read 1 reference strings 741s Checked 0 alignments, 0 edits 741s --------------- 741s PASSED 741s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 741s /usr/bin/bowtie2 -i C,1.11675136486248 -k 2 --trim3 6 --score-min L,5.02126235319641,5.34090439508524 --mm --rfg 4.69761667414448,17.8676291088334 --norc --cp-min 4 --large-index --cp-ival 1 --local -r -p 4 -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 741s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '8' because it was < 2 characters long 741s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '10' because it was < 2 characters long 741s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '19' because it was < 2 characters long 741s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '23' because it was < 2 characters long 741s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '26' because it was < 2 characters long 741s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '34' because it was < 2 characters long 741s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '43' because it was < 2 characters long 741s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '53' because it was < 2 characters long 741s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '61' because it was < 2 characters long 741s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '66' because it was < 2 characters long 741s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '67' because it was < 2 characters long 741s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '75' because it was < 2 characters long 741s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '78' because it was < 2 characters long 741s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '80' because it was < 2 characters long 741s 81 reads; of these: 741s 81 (100.00%) were unpaired; of these: 741s 81 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 741s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 741s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 741s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 741s /usr/bin/bowtie2 -i C,1.11675136486248 -k 2 --trim3 6 --score-min L,5.02126235319641,5.34090439508524 --mm --rfg 4.69761667414448,17.8676291088334 --norc --cp-min 4 --large-index --cp-ival 1 --local -r -p 2 -x /tmp/Sim.pm.pBDT5Pxz --reorder /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 741s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '8' because it was < 2 characters long 741s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '10' because it was < 2 characters long 741s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '19' because it was < 2 characters long 741s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '23' because it was < 2 characters long 741s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '26' because it was < 2 characters long 741s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '34' because it was < 2 characters long 741s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '43' because it was < 2 characters long 741s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '53' because it was < 2 characters long 741s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '61' because it was < 2 characters long 741s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '66' because it was < 2 characters long 741s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '67' because it was < 2 characters long 741s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '75' because it was < 2 characters long 741s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '78' because it was < 2 characters long 741s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '80' because it was < 2 characters long 741s 81 reads; of these: 741s 81 (100.00%) were unpaired; of these: 741s 81 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 741s Flattened IUPAC characters 741s Mutating sequence Sim.pm.1 741s Introducing 19 SNPs, 0/2 ref/read gaps, and 1 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutating sequence Sim.pm.2 741s Introducing 15 SNPs, 1/1 ref/read gaps, and 0 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutated reference genome to subject genome 741s SNPs introduced: 34 741s Reference gaps introduced: 1 741s Read gaps introduced: 3 741s Rearrangements introduced: 1 741s Created read sampler 741s Sampling 79 reads 741s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 741s *** Run 26 of 100 741s /usr/bin/bowtie2 --large-index --cp-min 7 --score-min L,9.18176417073699,4.86797125627173 --mm --rdg 28.7047702287815 --n-ceil 1.15126600622088,0.0361577596391596 --trim5 3 -M 7 --cp-ival 3 --local -i S,1.05231187140872 --trim3 3 --rfg 41.9628044896938,4.19901222964564 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 741s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 741s parsing sequence Sim.pm.1... 741s parsing sequence Sim.pm.2... 741s Parsed 166 reference bases 741s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 741s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '3' because it was < 2 characters long 741s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '7' because it was < 2 characters long 741s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '8' because it was < 2 characters long 741s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '10' because it was < 2 characters long 741s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '14' because it was < 2 characters long 741s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '15' because it was < 2 characters long 741s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '16' because it was < 2 characters long 741s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '17' because it was < 2 characters long 741s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '27' because it was < 2 characters long 741s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '28' because it was < 2 characters long 741s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '29' because it was < 2 characters long 741s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '32' because it was < 2 characters long 741s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '38' because it was < 2 characters long 741s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '43' because it was < 2 characters long 741s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '44' because it was < 2 characters long 741s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '46' because it was < 2 characters long 741s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '47' because it was < 2 characters long 741s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 741s Warning: skipping mate #2 of read '55' because it was < 2 characters long 741s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '56' because it was < 2 characters long 741s Warning: skipping mate #1 of read '59' because length (1) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '59' because it was < 2 characters long 741s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '75' because it was < 2 characters long 741s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 741s Warning: skipping mate #1 of read '78' because it was < 2 characters long 741s Read 50 alignments... 741s 79 reads; of these: 741s 70 (88.61%) were paired; of these: 741s 70 (100.00%) aligned concordantly 0 times 741s 0 (0.00%) aligned concordantly exactly 1 time 741s 0 (0.00%) aligned concordantly >1 times 741s ---- 741s 70 pairs aligned concordantly 0 times; of these: 741s 0 (0.00%) aligned discordantly 1 time 741s ---- 741s 70 pairs aligned 0 times concordantly or discordantly; of these: 741s 140 mates make up the pairs; of these: 741s 140 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 9 (11.39%) were unpaired; of these: 741s 9 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s Read 100 alignments... 741s Read 150 alignments... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s --- Summary --- 741s Read 1 reference strings 741s Checked 0 alignments, 0 edits 741s --------------- 741s PASSED 741s ALSO checking that bowtie2 and bowtie2-align match up 741s /usr/bin/bowtie2 --large-index --cp-min 7 --score-min L,9.18176417073699,4.86797125627173 --mm --rdg 28.7047702287815 --n-ceil 1.15126600622088,0.0361577596391596 --trim5 3 -M 7 --cp-ival 3 --local -i S,1.05231187140872 --trim3 3 --rfg 41.9628044896938,4.19901222964564 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 742s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 742s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '3' because it was < 2 characters long 742s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '7' because it was < 2 characters long 742s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '8' because it was < 2 characters long 742s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '10' because it was < 2 characters long 742s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '14' because it was < 2 characters long 742s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '15' because it was < 2 characters long 742s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '16' because it was < 2 characters long 742s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '17' because it was < 2 characters long 742s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '27' because it was < 2 characters long 742s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '28' because it was < 2 characters long 742s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '29' because it was < 2 characters long 742s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '32' because it was < 2 characters long 742s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '38' because it was < 2 characters long 742s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '43' because it was < 2 characters long 742s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '44' because it was < 2 characters long 742s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '46' because it was < 2 characters long 742s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '47' because it was < 2 characters long 742s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '55' because it was < 2 characters long 742s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '56' because it was < 2 characters long 742s Warning: skipping mate #1 of read '59' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '59' because it was < 2 characters long 742s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '75' because it was < 2 characters long 742s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '78' because it was < 2 characters long 742s 79 reads; of these: 742s 70 (88.61%) were paired; of these: 742s 70 (100.00%) aligned concordantly 0 times 742s 0 (0.00%) aligned concordantly exactly 1 time 742s 0 (0.00%) aligned concordantly >1 times 742s ---- 742s 70 pairs aligned concordantly 0 times; of these: 742s 0 (0.00%) aligned discordantly 1 time 742s ---- 742s 70 pairs aligned 0 times concordantly or discordantly; of these: 742s 140 mates make up the pairs; of these: 742s 140 (100.00%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 0 (0.00%) aligned >1 times 742s 9 (11.39%) were unpaired; of these: 742s 9 (100.00%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 0 (0.00%) aligned >1 times 742s 0.00% overall alignment rate 742s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 742s /usr/bin/bowtie2 --large-index --cp-min 7 --score-min L,9.18176417073699,4.86797125627173 --mm --rdg 28.7047702287815 --n-ceil 1.15126600622088,0.0361577596391596 --trim5 3 -M 7 --cp-ival 3 --local -i S,1.05231187140872 --trim3 3 --rfg 41.9628044896938,4.19901222964564 -f -p 2 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 742s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 742s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 742s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '3' because it was < 2 characters long 742s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '7' because it was < 2 characters long 742s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '8' because it was < 2 characters long 742s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '10' because it was < 2 characters long 742s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '14' because it was < 2 characters long 742s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '15' because it was < 2 characters long 742s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '16' because it was < 2 characters long 742s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '17' because it was < 2 characters long 742s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '27' because it was < 2 characters long 742s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '28' because it was < 2 characters long 742s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '29' because it was < 2 characters long 742s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '32' because it was < 2 characters long 742s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '38' because it was < 2 characters long 742s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '43' because it was < 2 characters long 742s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '44' because it was < 2 characters long 742s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '46' because it was < 2 characters long 742s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '47' because it was < 2 characters long 742s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '55' because it was < 2 characters long 742s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '56' because it was < 2 characters long 742s Warning: skipping mate #1 of read '59' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '59' because it was < 2 characters long 742s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '75' because it was < 2 characters long 742s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '78' because it was < 2 characters long 742s 79 reads; of these: 742s 70 (88.61%) were paired; of these: 742s 70 (100.00%) aligned concordantly 0 times 742s 0 (0.00%) aligned concordantly exactly 1 time 742s 0 (0.00%) aligned concordantly >1 times 742s ---- 742s 70 pairs aligned concordantly 0 times; of these: 742s 0 (0.00%) aligned discordantly 1 time 742s ---- 742s 70 pairs aligned 0 times concordantly or discordantly; of these: 742s 140 mates make up the pairs; of these: 742s 140 (100.00%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 0 (0.00%) aligned >1 times 742s 9 (11.39%) were unpaired; of these: 742s 9 (100.00%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 0 (0.00%) aligned >1 times 742s 0.00% overall alignment rate 742s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 742s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 742s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 742s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 742s /usr/bin/bowtie2 --large-index --cp-min 7 --score-min L,9.18176417073699,4.86797125627173 --mm --rdg 28.7047702287815 --n-ceil 1.15126600622088,0.0361577596391596 --trim5 3 -M 7 --cp-ival 3 --local -i S,1.05231187140872 --trim3 3 --rfg 41.9628044896938,4.19901222964564 -f -p 4 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 742s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 742s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '3' because it was < 2 characters long 742s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '7' because it was < 2 characters long 742s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '8' because it was < 2 characters long 742s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '10' because it was < 2 characters long 742s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '14' because it was < 2 characters long 742s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '15' because it was < 2 characters long 742s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '16' because it was < 2 characters long 742s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '17' because it was < 2 characters long 742s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '27' because it was < 2 characters long 742s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '28' because it was < 2 characters long 742s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '29' because it was < 2 characters long 742s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '32' because it was < 2 characters long 742s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '38' because it was < 2 characters long 742s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '43' because it was < 2 characters long 742s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '44' because it was < 2 characters long 742s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '46' because it was < 2 characters long 742s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '47' because it was < 2 characters long 742s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '55' because it was < 2 characters long 742s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '56' because it was < 2 characters long 742s Warning: skipping mate #1 of read '59' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '59' because it was < 2 characters long 742s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '75' because it was < 2 characters long 742s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '78' because it was < 2 characters long 742s 79 reads; of these: 742s 70 (88.61%) were paired; of these: 742s 70 (100.00%) aligned concordantly 0 times 742s 0 (0.00%) aligned concordantly exactly 1 time 742s 0 (0.00%) aligned concordantly >1 times 742s ---- 742s 70 pairs aligned concordantly 0 times; of these: 742s 0 (0.00%) aligned discordantly 1 time 742s ---- 742s 70 pairs aligned 0 times concordantly or discordantly; of these: 742s 140 mates make up the pairs; of these: 742s 140 (100.00%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 0 (0.00%) aligned >1 times 742s 9 (11.39%) were unpaired; of these: 742s 9 (100.00%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 0 (0.00%) aligned >1 times 742s 0.00% overall alignment rate 742s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 742s Flattened IUPAC characters 742s Mutating sequence Sim.pm.2 742s Introducing 14 SNPs, 0/0 ref/read gaps, and 1 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutating sequence Sim.pm.1 742s Introducing 0 SNPs, 4/0 ref/read gaps, and 1 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutated reference genome to subject genome 742s SNPs introduced: 14 742s Reference gaps introduced: 4 742s Read gaps introduced: 0 742s Rearrangements introduced: 2 742s Created read sampler 742s Sampling 39 reads 742s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 742s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 742s parsing sequence Sim.pm.1... 742s parsing sequence Sim.pm.2... 742s Parsed 166 reference bases 742s *** Run 27 of 100 742s /usr/bin/bowtie2 -M 2 --trim5 8 --local --cp-ival 1 --trim3 2 --large-index --cp-min 4 --np 1 --score-min L,8.62393923897056,1.93966628837941 --gbar 1 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 742s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 742s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '2' because it was < 2 characters long 742s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '6' because it was < 2 characters long 742s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '7' because it was < 2 characters long 742s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '13' because it was < 2 characters long 742s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '19' because it was < 2 characters long 742s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '26' because it was < 2 characters long 742s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '34' because it was < 2 characters long 742s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '35' because it was < 2 characters long 742s 39 reads; of these: 742s 26 (66.67%) were paired; of these: 742s 26 (100.00%) aligned concordantly 0 times 742s 0 (0.00%) aligned concordantly exactly 1 time 742s 0 (0.00%) aligned concordantly >1 times 742s ---- 742s 26 pairs aligned concordantly 0 times; of these: 742s 0 (0.00%) aligned discordantly 1 time 742s ---- 742s 26 pairs aligned 0 times concordantly or discordantly; of these: 742s 52 mates make up the pairs; of these: 742s 52 (100.00%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 0 (0.00%) aligned >1 times 742s 13 (33.33%) were unpaired; of these: 742s 13 (100.00%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 0 (0.00%) aligned >1 times 742s 0.00% overall alignment rate 742s Read 50 alignments... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s --- Summary --- 742s Read 1 reference strings 742s Checked 0 alignments, 0 edits 742s --------------- 742s PASSED 742s Flattened IUPAC characters 742s Mutating sequence Sim.pm.1 742s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 742s *** Run 28 of 100 742s /usr/bin/bowtie2 -D 9 --score-min L,1.56049231330019,3.03046474679816 --trim3 6 --rfg 21.7958246798465,6.7076895698689 --trim5 1 --large-index -a --cp-min 2 --cp-ival 1 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutating sequence Sim.pm.2 742s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutated reference genome to subject genome 742s SNPs introduced: 14 742s Reference gaps introduced: 0 742s Read gaps introduced: 1 742s Rearrangements introduced: 1 742s Created read sampler 742s Sampling 169 reads 742s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 742s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 742s parsing sequence Sim.pm.1... 742s parsing sequence Sim.pm.2... 742s Parsed 166 reference bases 742s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 742s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '12' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 742s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '17' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 742s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '19' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 742s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '23' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 742s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '26' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 742s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '29' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 742s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '34' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 742s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '38' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 742s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '55' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 742s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '63' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 742s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '66' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 742s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '67' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 742s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '68' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 742s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '75' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 742s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '79' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 742s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '81' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 742s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '84' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 742s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '104' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 742s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '108' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 742s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '117' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 742s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '124' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 742s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '130' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 742s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '131' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 742s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '133' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 742s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '137' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 742s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '143' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 742s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '145' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 742s Warning: skipping read '148' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '148' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 742s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '158' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 742s Read 50 alignments... 742s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 742s Warning: skipping read '160' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '160' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 742s Warning: skipping read '162' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '162' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 742s Warning: skipping read '168' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '168' because it was < 2 characters long 742s Read 100 alignments... 742s 169 reads; of these: 742s 169 (100.00%) were unpaired; of these: 742s 149 (88.17%) aligned 0 times 742s 8 (4.73%) aligned exactly 1 time 742s 12 (7.10%) aligned >1 times 742s 11.83% overall alignment rate 742s Read 150 alignments... 742s Read 200 alignments... 742s Read 250 alignments... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GAGTGGGCGGTTGA 742s GAGTGGGCGGTTGA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AGTGGGCGG 742s AGTGGGCGG 742s Processing line... 742s Processing line... 742s GCT 742s GCT 742s Processing line... 742s GCT 742s GCT 742s Processing line... 742s GCT 742s GCT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 742s GCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 742s Processing line... 742s GCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 742s GCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 742s Processing line... 742s Processing line... 742s TCGG 742s TCGG 742s Processing line... 742s TCGG 742s TCGG 742s Processing line... 742s TCGG 742s TCGG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TGATCGGGAGTGGGCGGTT 742s TGATCGGGAGTGGGCGGTT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GTTGCTTTAGGAGG 742s GTTGCTTTAGGAGG 742s Processing line... 742s GTTGCTTTAGGAGG 742s GTTGCTTTAGGAGG 742s Processing line... 742s GTTGCTTTAGGAGG 742s GTTGCTTTAGGAGG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s CC 742s CC 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s CC 742s CC 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s CC 742s CC 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s GG 742s GG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GGCCGGGGCGGCGGTTGCTTTAGG 742s GGCCGGGGCGGCGGTTGCTTTAGG 742s Processing line... 742s GGCCGGGGCGGCGGTTGCTTTAGG 742s GGCCGGGGCGGCGGTTGCTTTAGG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GCGGTTGCTTTAGGAGGGATGGGCCGGGGCG 742s GCGGTTGCTTTAGGAGGGATGGGCCGGGGCG 742s Processing line... 742s GCGGTTGCTTTAGGAGGGATGGGCCGGGGCG 742s GCGGTTGCTTTAGGAGGGATGGGCCGGGGCG 742s Processing line... 742s Processing line... 742s TGTAGTGGCGGTCTGAG 742s TGTAGTGGCGGTCTGAG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GGGCCGGGGCGG 742s GGGCCGGGGCGG 742s Processing line... 742s GGGCCGGGGCGG 742s GGGCCGGGGCGG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TTGTAGT 742s TTGTAGT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CATTGTAGTGGCGGTCTGAG 742s CATTGTAGTGGCGGTCTGAG 742s Processing line... 742s CGGT 742s CGGT 742s Processing line... 742s CGGT 742s CGGT 742s Processing line... 742s CGGT 742s CGGT 742s Processing line... 742s CGGT 742s CGGT 742s Processing line... 742s CGGT 742s CGGT 742s Processing line... 742s CGGT 742s CGGT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GGCGGTTGACT 742s GGCGGTTGACT 742s Processing line... 742s GGCGGTTGACT 742s GGCGGTTGACT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CATTGTAGTGGCGGTCT 742s CATTGTAGTGGCGGTCT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CGGTTGACTTTCGGC 742s CGGTTGACTTTCGGC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s /usr/bin/bowtie2 -D 9 --score-min L,1.56049231330019,3.03046474679816 --trim3 6 --rfg 21.7958246798465,6.7076895698689 --trim5 1 --large-index -a --cp-min 2 --cp-ival 1 -r -p 2 -x /tmp/Sim.pm.pBDT5Pxz --reorder /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s --- Summary --- 742s Read 1 reference strings 742s Checked 111 alignments, 0 edits 742s --------------- 742s PASSED 742s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 742s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 742s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '12' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 742s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '17' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 742s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '19' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 742s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '23' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 742s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '26' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 742s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '29' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 742s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '34' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 742s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '38' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 742s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '55' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 742s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '63' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 742s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '66' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 742s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '67' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 742s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '68' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 742s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '75' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 742s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '79' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 742s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '81' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 742s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '84' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 742s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '104' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 742s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '108' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 742s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '117' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 742s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '124' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 742s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '130' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 742s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '131' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 742s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '133' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 742s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '137' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 742s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '143' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 742s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '145' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 742s Warning: skipping read '148' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '148' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 742s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '158' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 742s Warning: skipping read '160' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '160' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 742s Warning: skipping read '162' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '162' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 742s Warning: skipping read '168' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '168' because it was < 2 characters long 742s 169 reads; of these: 742s 169 (100.00%) were unpaired; of these: 742s 149 (88.17diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 742s %) aligned 0 times 742s 8 (4.73%) aligned exactly 1 time 742s 12 (7.10%) aligned >1 times 742s 11.83% overall alignment rate 742s Flattened IUPAC characters 742s Mutating sequence Sim.pm.2 742s Introducing 11 SNPs, 1/3 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutating sequence Sim.pm.1 742s Introducing 18 SNPs, 3/2 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutated reference genome to subject genome 742s SNPs introduced: 29 742s Reference gaps introduced: 4 742s Read gaps introduced: 5 742s Rearrangements introduced: 0 742s Created read sampler 742s Sampling 137 reads 742s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 742s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 742s parsing sequence Sim.pm.1... 742s parsing sequence Sim.pm.2... 742s Parsed 166 reference bases 742s *** Run 29 of 100 742s /usr/bin/bowtie2 --cp-ival 3 --local --mp 8.86169576656266,3.52246690886546 --trim3 8 --rfg 40.5517380996131 --cp-min 7 --np 3 --large-index -D 8 -k 2 --score-min L,9.36141012223431,8.24989600304568 --rdg 48.4978565728841,8.74392490984575 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 742s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '2' because it was < 2 characters long 742s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '27' because it was < 2 characters long 742s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '34' because it was < 2 characters long 742s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '37' because it was < 2 characters long 742s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '39' because it was < 2 characters long 742s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '40' because it was < 2 characters long 742s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '41' because it was < 2 characters long 742s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '43' because it was < 2 characters long 742s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '47' because it was < 2 characters long 742s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '48' because it was < 2 characters long 742s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '53' because it was < 2 characters long 742s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '54' because it was < 2 characters long 742s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '65' because it was < 2 characters long 742s Read 50 alignments... 742s Read 100 alignments... 742s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '66' because it was < 2 characters long 742s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '86' because it was < 2 characters long 742s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '90' because it was < 2 characters long 742s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '99' because it was < 2 characters long 742s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '104' because it was < 2 characters long 742s Warning: skipping mate #1 of read '108' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '108' because it was < 2 characters long 742s Read 150 alignments... 742s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '116' because it was < 2 characters long 742s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '117' because it was < 2 characters long 742s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '118' because it was < 2 characters long 742s Warning: skipping mate #1 of read '127' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '127' because it was < 2 characters long 742s Warning: skipping mate #1 of read '131' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '131' because it was < 2 characters long 742s Read 200 alignments... 742s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '136' because it was < 2 characters long 742s 137 reads; of these: 742s 121 (88.32%) were paired; of these: 742s 121 (100.00%) aligned concordantly 0 times 742s 0 (0.00%) aligned concordantly exactly 1 time 742s 0 (0.00%) aligned concordantly >1 times 742s ---- 742s 121 pairs aligned concordantly 0 times; of these: 742s 0 (0.00%) aligned discordantly 1 time 742s ---- 742s 121 pairs aligned 0 times concordantly or discordantly; of these: 742s 242 mates make up the pairs; of these: 742s 242 (100.00%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 0 (0.00%) aligned >1 times 742s 16 (11.68%) were unpaired; of these: 742s 16 (100.00%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 0 (0.00%) aligned >1 times 742s 0.00% overall alignment rate 742s Read 250 alignments... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing 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Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing 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line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s /usr/bin/bowtie2 --cp-ival 3 --local --mp 8.86169576656266,3.52246690886546 --trim3 8 --rfg 40.5517380996131 --cp-min 7 --np 3 --large-index -D 8 -k 2 --score-min L,9.36141012223431,8.24989600304568 --rdg 48.4978565728841,8.74392490984575 -q -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 742s --- Summary --- 742s Read 1 reference strings 742s Checked 0 alignments, 0 edits 742s --------------- 742s PASSED 742s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 742s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '2' because it was < 2 characters long 742s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '27' because it was < 2 characters long 742s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '34' because it was < 2 characters long 742s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '37' because it was < 2 characters long 742s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '39' because it was < 2 characters long 742s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '40' because it was < 2 characters long 742s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '41' because it was < 2 characters long 742s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '43' because it was < 2 characters long 742s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '47' because it was < 2 characters long 742s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '48' because it was < 2 characters long 742s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '53' because it was < 2 characters long 742s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '54' because it was < 2 characters long 742s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '65' because it was < 2 characters long 742s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '66' because it was < 2 characters long 742s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '86' because it was < 2 characters long 742s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '90' because it was < 2 characters long 742s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '99' because it was < 2 characters long 742s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '104' because it was < 2 characters long 742s Warning: skipping mate #1 of read '108' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '108' because it was < 2 characters long 742s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '116' because it was < 2 characters long 742s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '117' because it was < 2 characters long 742s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '118' because it was < 2 characters long 742s Warning: skipping mate #1 of read '127' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '127' because it was < 2 characters long 742s Warning: skipping mate #1 of read '131' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '131' because it was < 2 characters long 742s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '136' because it was < 2 characters long 742s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 742s 137 reads; of these: 742s 121 (88.32%) were paired; of these: 742s 121 (100.00%) aligned concordantly 0 times 742s 0 (0.00%) aligned concordantly exactly 1 time 742s 0 (0.00%) aligned concordantly >1 times 742s ---- 742s 121 pairs aligned concordantly 0 times; of these: 742s 0 (0.00%) aligned discordantly 1 time 742s ---- 742s 121 pairs aligned 0 times concordantly or discordantly; of these: 742s 242 mates make up the pairs; of these: 742s 242 (100.00%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 0 (0.00%) aligned >1 times 742s 16 (11.68%) were unpaired; of these: 742s 16 (100.00%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 0 (0.00%) aligned >1 times 742s 0.00% overall alignment rate 742s Flattened IUPAC characters 742s Mutating sequence Sim.pm.1 742s Introducing 9 SNPs, 0/1 ref/read gaps, and 2 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutating sequence Sim.pm.2 742s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutated reference genome to subject genome 742s SNPs introduced: 12 742s Reference gaps introduced: 0 742s Read gaps introduced: 1 742s Rearrangements introduced: 2 742s Created read sampler 742s Sampling 33 reads 742s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 742s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 742s parsing sequence Sim.pm.1... 742s parsing sequence Sim.pm.2... 742s Parsed 166 reference bases 742s *** Run 30 of 100 742s /usr/bin/bowtie2 -R 3 -k 2 --ma 38.328352152328 --score-min L,1.55494090317282,4.57158074881153 --mm --rdg 10.2522555628986,16.6769875127561 --np 2 --cp-min 5 --large-index --mp 6.98771631762194,3.25344065089824 -i L,0.241364930298188 --trim3 6 --nofw --trim5 1 --n-ceil 0.901413508281181,0.385201193737845 --cp-ival 1 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 742s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 742s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 742s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '14' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 742s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '20' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 742s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '21' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 742s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '22' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 742s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '24' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 742s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '26' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 742s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '31' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 742s 33 reads; of these: 742s 33 (100.00%) were unpaired; of these: 742s 30 (90.91%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 3 (9.09%) aligned >1 times 742s 9.09% overall alignment rate 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TTCG 742s TTCG 742s Processing line... 742s TTCG 742s TTCG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GTTGCTTTAGGAGGGATGGGCCGGGGCG 742s GTTGCTTTAGGAGGGATGGGCCGGGGCG 742s Processing line... 742s GTTGCTTTAGGAGGGATGGGCCGGGGCG 742s GTTGCTTTAGGAGGGATGGGCCGGGGCG 742s Processing line... 742s GGATG 742s GGATG 742s Processing line... 742s GGATG 742s GGATG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s --- Summary --- 742s Read 1 reference strings 742s Checked 6 alignments, 0 edits 742s --------------- 742s PASSED 742s Flattened IUPAC characters 742s Mutating sequence Sim.pm.2 742s Introducing 14 SNPs, 0/0 ref/read gaps, and 1 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutating sequence Sim.pm.1 742s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutated reference genome to subject genome 742s SNPs introduced: 15 742s Reference gaps introduced: 1 742s Read gaps introduced: 0 742s Rearrangements introduced: 1 742s Created read sampler 742s Sampling 108 reads 742s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 742s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 742s parsing sequence Sim.pm.1... 742s *** Run 31 of 100 742s /usr/bin/bowtie2 --cp-min 5 --trim3 7 --score-min L,4.32992009401471,4.9953890599348 --large-index --cp-ival 1 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 742s parsing sequence Sim.pm.2... 742s Parsed 166 reference bases 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 743s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '5' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 743s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '24' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 743s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '29' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 743s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '30' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 743s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '42' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 743s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '45' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 743s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '48' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 743s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '52' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 743s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '61' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 743s Read 50 alignments... 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 743s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '66' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 743s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '81' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 743s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '87' because it was < 2 characters long 743s Warning: skipping mate #2 of read '87' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 743s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '97' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 743s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '99' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 743s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '103' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 743s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '104' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 743s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '107' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 743s Read 100 alignments... 743s 108 reads; of these: 743s 89 (82.41%) were paired; of these: 743s 88 (98.88%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 1 (1.12%) aligned concordantly >1 times 743s ---- 743s 88 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 88 pairs aligned 0 times concordantly or discordantly; of these: 743s 176 mates make up the pairs; of these: 743s 147 (83.52%) aligned 0 times 743s 4 (2.27%) aligned exactly 1 time 743s 25 (14.20%) aligned >1 times 743s 19 (17.59%) were unpaired; of these: 743s 15 (78.95%) aligned 0 times 743s 1 (5.26%) aligned exactly 1 time 743s 3 (15.79%) aligned >1 times 743s 17.77% overall alignment rate 743s Read 150 alignments... 743s Read 200 alignments... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GT 743s GT 743s Processing line... 743s Processing line... 743s TGCTTTAGGAGGGATGGGCCGGGGCGGCGGTT 743s TGCTTTAGGAGGGATGGGCCGGGGCGGCGGTT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TTGTAG 743s TTGTAG 743s Processing line... 743s Processing line... 743s AT 743s AT 743s Processing line... 743s Processing line... 743s GCCGGGGCGGCGGTTGCTTTAGG 743s GCCGGGGCGGCGGTTGCTTTAGG 743s Processing line... 743s Processing line... 743s CGGTTGCTTTAGGAGG 743s CGGTTGCTTTAGGAGG 743s Processing line... 743s Processing line... 743s GCCGGGGCGGCGGTTGCTTTAGGAGG 743s GCCGGGGCGGCGGTTGCTTTAGGAGG 743s Processing line... 743s Processing line... 743s TAGGAGGGA 743s TAGGAGGGA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGC 743s GGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TGGGCCGGGGCGGCGGTTGCTTTA 743s TGGGCCGGGGCGGCGGTTGCTTTA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TGGCGGTCTGAG 743s TGGCGGTCTGAG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGGGCGGCGGTTGCTTTAGGAGGGATGGGCCG 743s GGGGCGGCGGTTGCTTTAGGAGGGATGGGCCG 743s Processing line... 743s CGA 743s CGA 743s Processing line... 743s Processing line... 743s GTG 743s GTG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TAGGA 743s TAGGA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TTAGGA 743s TTAGGA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CCGGGGCGGCGG 743s CCGGGGCGGCGG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s ATTGTAGTGGCGGTCTGA 743s ATTGTAGTGGCGGTCTGA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTT 743s TTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GAGGGATGGGCCGGGGCGGC 743s GAGGGATGGGCCGGGGCGGC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGTTGACTTTCG 743s GGTTGACTTTCG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGGCGGCGGTTGCTTTA 743s GGGCGGCGGTTGCTTTA 743s Processing line... 743s Processing line... 743s GTC 743s GTC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGTTGACTTTC 743s GGTTGACTTTC 743s Processing line... 743s CGG 743s CGG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s AGTGG 743s AGTGG 743s Processing line... 743s Processing line... 743s CGGTTGCTTTAGGAGGGA 743s CGGTTGCTTTAGGAGGGA 743s Processing line... 743s Processing line... 743s /usr/bin/bowtie2 --cp-min 5 --trim3 7 --score-min L,4.32992009401471,4.9953890599348 --large-index --cp-ival 1 -f -p 4 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GC 743s GC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGG 743s GGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGGCGG 743s GGGCGG 743s Processing line... 743s Processing line... 743s Processing line... 743s GGGCCGGG 743s GGGCCGGG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGTTGC 743s GGTTGC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TGGG 743s TGGG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GCG 743s GCG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGTTGCTTTAGGAGGGATGG 743s GGTTGCTTTAGGAGGGATGG 743s Processing line... 743s --- Summary --- 743s Read 1 reference strings 743s Checked 35 alignments, 0 edits 743s --------------- 743s PASSED 743s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 743s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '5' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 743s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '24' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 743s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '29' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 743s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '30' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 743s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '42' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 743s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '45' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 743s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '48' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 743s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '52' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 743s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '61' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 743s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '66' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 743s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '81' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 743s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '87' because it was < 2 characters long 743s Warning: skipping mate #2 of read '87' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 743s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '97' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 743s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '99' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 743s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '103' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 743s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '104' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 743s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '107' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 743s 108 reads; of these: 743s 89 (82.41%) were paired; of these: 743s 88 (98.88%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 1 (1.12%) aligned concordantly >1 times 743s ---- 743s 88 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 88 pairs aligned 0 times concordantly or discordantly; of these: 743s 176 mates make up the pairs; of these: 743s 147 (83.52%) aligned 0 times 743s 4 (2.27%) aligned exactly 1 time 743s 25 (14.20%) aligned >1 times 743s 19 (17.59%) were unpaired; of these: 743s 15 (78.95%) aligned 0 times 743s 1 (5.26%) aligned exactly 1 time 743s 3 (15.79%) aligned >1 times 743s 17.77% overall alignment rate 743s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 743s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 743s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 743s Flattened IUPAC characters 743s Mutating sequence Sim.pm.2 743s Introducing 20 SNPs, 4/1 ref/read gaps, and 2 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutating sequence Sim.pm.1 743s Introducing 8 SNPs, 2/1 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutated reference genome to subject genome 743s SNPs introduced: 28 743s Reference gaps introduced: 6 743s Read gaps introduced: 2 743s Rearrangements introduced: 2 743s Created read sampler 743s Sampling 74 reads 743s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 743s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 743s parsing sequence Sim.pm.1... 743s parsing sequence Sim.pm.2... 743s *** Run 32 of 100 743s /usr/bin/bowtie2 --n-ceil 0.167331884020572,0.252694132960868 --cp-ival 1 --local -k 3 --score-min L,1.56176695355689,6.85409137913853 --mm --rdg 20.1417671297911 --np 2 --cp-min 3 --large-index -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 743s Parsed 166 reference bases 743s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '32' because it was < 2 characters long 743s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '44' because it was < 2 characters long 743s 74 reads; of these: 743s 74 (100.00%) were paired; of these: 743s 74 (100.00%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 0 (0.00%) aligned concordantly >1 times 743s ---- 743s 74 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 74 pairs aligned 0 times concordantly or discordantly; of these: 743s 148 mates make up the pairs; of these: 743s 148 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 0.00% overall alignment rate 743s Read 50 alignments... 743s Read 100 alignments... 743s Read 150 alignments... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s --- Summary --- 743s Read 1 reference strings 743s Checked 0 alignments, 0 edits 743s --------------- 743s PASSED 743s Flattened IUPAC characters 743s Mutating sequence Sim.pm.2 743s Introducing 10 SNPs, 0/2 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutating sequence Sim.pm.1 743s Introducing 7 SNPs, 1/0 ref/read gaps, and 2 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutated reference genome to subject genome 743s SNPs introduced: 17 743s Reference gaps introduced: 1 743s Read gaps introduced: 2 743s Rearrangements introduced: 2 743s Created read sampler 743s Sampling 58 reads 743s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 743s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 743s parsing sequence Sim.pm.1... 743s parsing sequence Sim.pm.2... 743s Parsed 166 reference bases 743s *** Run 33 of 100 743s /usr/bin/bowtie2 --rfg 15.5636451583867,3.80114438901528 --rdg 23.4046676500685,1.98507926600601 -N 1 -L22 --trim3 4 --score-min L,3.93385627743685,9.45442016172489 --cp-ival 1 --local --np 2 --cp-min 6 --large-index --qseq -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.qseq 743s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 743s 58 reads; of these: 743s 58 (100.00%) were unpaired; of these: 743s 58 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 0.00% overall alignment rate 743s Read 50 alignments... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s /usr/bin/bowtie2 --rfg 15.5636451583867,3.80114438901528 --rdg 23.4046676500685,1.98507926600601 -N 1 -L22 --trim3 4 --score-min L,3.93385627743685,9.45442016172489 --cp-ival 1 --local --np 2 --cp-min 6 --large-index --qseq -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s --- Summary --- 743s Read 1 reference strings 743s Checked 0 alignments, 0 edits 743s --------------- 743s PASSED 743s ALSO checking that bowtie2 and bowtie2-align match up 743s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 743s 58 reads; of these: 743s 58 (100.00%) were unpaired; of these: 743s 58 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 0.00% overall alignment rate 743s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 743s /usr/bin/bowtie2 --rfg 15.5636451583867,3.80114438901528 --rdg 23.4046676500685,1.98507926600601 -N 1 -L22 --trim3 4 --score-min L,3.93385627743685,9.45442016172489 --cp-ival 1 --local --np 2 --cp-min 6 --large-index --qseq -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder /tmp/Sim.pm.pBDT5Pxz_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 743s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 743s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 743s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 743s 58 reads; of these: 743s 58 (100.00%) were unpaired; of these: 743s 58 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 0.00% overall alignment rate 743s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 743s Flattened IUPAC characters 743s Mutating sequence Sim.pm.1 743s Introducing 13 SNPs, 4/0 ref/read gaps, and 2 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutating sequence Sim.pm.2 743s Introducing 13 SNPs, 1/0 ref/read gaps, and 1 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutated reference genome to subject genome 743s SNPs introduced: 26 743s Reference gaps introduced: 5 743s Read gaps introduced: 0 743s Rearrangements introduced: 3 743s Created read sampler 743s Sampling 130 reads 743s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 743s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 743s parsing sequence Sim.pm.1... 743s parsing sequence Sim.pm.2... 743s Parsed 166 reference bases 743s *** Run 34 of 100 743s /usr/bin/bowtie2 --cp-ival 1 --trim5 4 --n-ceil 0.362800076761286,0.486724949149238 --norc -i C,4.36038064334186 --np 2 --cp-min 2 --large-index --mm --ma 6.75320448354929 --score-min L,7.02297500844713,5.83896094435439 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 743s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 743s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '14' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 743s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '20' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 743s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '31' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 743s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '38' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 743s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '45' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 743s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '47' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 743s Warning: skipping mate #1 of read '50' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '50' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 743s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '56' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 743s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '62' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 743s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '64' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '64' because it was < 2 characters long 743s Warning: skipping mate #2 of read '64' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 743s Warning: skipping mate #1 of read '66' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '66' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 743s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '73' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 743s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '75' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 743s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '80' because it was < 2 characters long 743s Read 50 alignments... 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 743s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '85' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 743s Warning: skipping mate #1 of read '102' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '102' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 743s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '107' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 743s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '112' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 743s Read 100 alignments... 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 743s Read 150 alignments... 743s Read 200 alignments... 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 743s Warning: skipping mate #1 of read '130' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '130' because it was < 2 characters long 743s 130 reads; of these: 743s 113 (86.92%) were paired; of these: 743s 113 (100.00%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 0 (0.00%) aligned concordantly >1 times 743s ---- 743s 113 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 113 pairs aligned 0 times concordantly or discordantly; of these: 743s 226 mates make up the pairs; of these: 743s 208 (92.04%) aligned 0 times 743s 6 (2.65%) aligned exactly 1 time 743s 12 (5.31%) aligned >1 times 743s 17 (13.08%) were unpaired; of these: 743s 15 (88.24%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 2 (11.76%) aligned >1 times 743s 8.23% overall alignment rate 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CTTTAGG 743s CTTTAGG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGGAT 743s GGGAT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGAGTGGGCGGT 743s GGAGTGGGCGGT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TCAT 743s TCAT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s AG 743s AG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CGGGTGTCATTGTAGTGGCGGTCTGAGGCC 743s CGGGTGTCATTGTAGTGGCGGTCTGAGGCC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TGGG 743s TGGG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CGGC 743s CGGC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TT 743s TT 743s Processing line... 743s AG 743s AG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TGGGCC 743s TGGGCC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GCGGTCT 743s GCGGTCT 743s Processing line... 743s Processing line... 743s CCG 743s CCG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGTTGCTTTAGGA 743s GGTTGCTTTAGGA 743s Processing line... 743s Processing line... 743s CGGCG 743s CGGCG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GA 743s GA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s /usr/bin/bowtie2 --cp-ival 1 --trim5 4 --n-ceil 0.362800076761286,0.486724949149238 --norc -i C,4.36038064334186 --np 2 --cp-min 2 --large-index --mm --ma 6.75320448354929 --score-min L,7.02297500844713,5.83896094435439 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TGTCATT 743s TGTCATT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGTCT 743s GGTCT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TT 743s TT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GC 743s GC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s --- Summary --- 743s Read 1 reference strings 743s Checked 20 alignments, 0 edits 743s --------------- 743s PASSED 743s ALSO checking that bowtie2 and bowtie2-align match up 743s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 743s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '14' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 743s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '20' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 743s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '31' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 743s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '38' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 743s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '45' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 743s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '47' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 743s Warning: skipping mate #1 of read '50' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '50' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 743s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '56' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 743s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '62' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 743s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '64' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '64' because it was < 2 characters long 743s Warning: skipping mate #2 of read '64' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 743s Warning: skipping mate #1 of read '66' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '66' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 743s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '73' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 743s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '75' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 743s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '80' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 743s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '85' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 743s Warning: skipping mate #1 of read '102' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '102' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 743s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '107' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 743s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '112' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 743s Warning: skipping mate #1 of read '130' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '130' because it was < 2 characters long 743s 130 reads; of these: 743s 113 (86.92%) were paired; of these: 743s 113 (100.00%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 0 (0.00%) aligned concordantly >1 times 743s ---- 743s 113 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 113 pairs aligned 0 times concordantly or discordantly; of these: 743s 226 mates make up the pairs; of these: 743s 208 (92.04%) aligned 0 times 743s 6 (2.65%) aligned exactly 1 time 743s 12 (5.31%) aligned >1 times 743s 17 (13.08%) were unpaired; of these: 743s 15 (88.24%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 2 (11.76%) aligned >1 times 743s 8.23% overall alignment rate 743s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 743s Flattened IUPAC characters 743s Mutating sequence Sim.pm.2 743s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutating sequence Sim.pm.1 743s Introducing 21 SNPs, 0/3 ref/read gaps, and 2 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutated reference genome to subject genome 743s SNPs introduced: 28 743s Reference gaps introduced: 0 743s Read gaps introduced: 4 743s Rearrangements introduced: 2 743s Created read sampler 743s Sampling 67 reads 743s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 743s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 743s parsing sequence Sim.pm.1... 743s parsing sequence Sim.pm.2... 743s Parsed 166 reference bases 743s *** Run 35 of 100 743s /usr/bin/bowtie2 -M 4 --large-index --cp-min 3 --cp-ival 1 --score-min L,3.85051626399806,7.93714006787953 --trim3 1 --ma 16.6142881257527 -N 0 -L25 -R 1 --rdg 49.7904022248388,2.00638521953614 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta 743s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 743s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 743s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 743s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '3' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 743s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '5' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 743s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '13' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 743s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '46' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 743s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '49' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 743s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '60' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 743s 67 reads; of these: 743s 67 (100.00%) were unpaired; of these: 743s 53 (79.10%) aligned 0 times 743s 4 (5.97%) aligned exactly 1 time 743s 10 (14.93%) aligned >1 times 743s 20.90% overall alignment rate 743s Read 50 alignments... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TGGGCCGGGGCG 743s TGGGCCGGGGCG 743s Processing line... 743s CCGG 743s CCGG 743s Processing line... 743s CTG 743s CTG 743s Processing line... 743s TGCT 743s TGCT 743s Processing line... 743s GG 743s GG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s /usr/bin/bowtie2 -M 4 --large-index --cp-min 3 --cp-ival 1 --score-min L,3.85051626399806,7.93714006787953 --trim3 1 --ma 16.6142881257527 -N 0 -L25 -R 1 --rdg 49.7904022248388,2.00638521953614 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GGGTGTCATTGTAG 743s GGGTGTCATTGTAG 743s Processing line... 743s CGGGTGTCATTGTA 743s CGGGTGTCATTGTA 743s Processing line... 743s CGGGGC 743s CGGGGC 743s Processing line... 743s GGCGGC 743s GGCGGC 743s Processing line... 743s GCGGTTGCTT 743s GCGGTTGCTT 743s Processing line... 743s GG 743s GG 743s Processing line... 743s Processing line... 743s Processing line... 743s GGTTGCTTTAG 743s GGTTGCTTTAG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s ATTG 743s ATTG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GCGG 743s GCGG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s --- Summary --- 743s Read 1 reference strings 743s Checked 14 alignments, 0 edits 743s --------------- 743s PASSED 743s ALSO checking that bowtie2 and bowtie2-align match up 743s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 743s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 743s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 743s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '3' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 743s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '5' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 743s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '13' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 743s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '46' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 743s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '49' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 743s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '60' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 743s 67 reads; of these: 743s 67 (100.00%) were unpaired; of these: 743s 53 (79.10%) aligned 0 times 743s 4 (5.97%) aligned exactly 1 time 743s 10 (14.93%) aligned >1 times 743s 20.90% overall alignment rate 743s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 743s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 743s /usr/bin/bowtie2 -M 4 --large-index --cp-min 3 --cp-ival 1 --score-min L,3.85051626399806,7.93714006787953 --trim3 1 --ma 16.6142881257527 -N 0 -L25 -R 1 --rdg 49.7904022248388,2.00638521953614 -f -p 2 -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 743s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 743s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 743s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 743s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '3' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 743s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '5' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 743s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '13' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 743s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '46' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 743s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '49' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 743s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '60' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 743s 67 reads; of these: 743s 67 (100.00%) were unpaired; of these: 743s 53 (79.10%) aligned 0 times 743s 4 (5.97%) aligned exactly 1 time 743s 10 (14.93%) aligned >1 times 743s 20.90% overall alignment rate 743s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 743s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 743s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 743s Flattened IUPAC characters 743s Mutating sequence Sim.pm.1 743s Introducing 5 SNPs, 3/2 ref/read gaps, and 1 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutating sequence Sim.pm.2 743s Introducing 15 SNPs, 0/0 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutated reference genome to subject genome 743s SNPs introduced: 20 743s Reference gaps introduced: 3 743s Read gaps introduced: 2 743s Rearrangements introduced: 1 743s Created read sampler 743s Sampling 61 reads 743s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 743s *** Run 36 of 100 743s /usr/bin/bowtie2 --local --cp-ival 3 --cp-min 2 --large-index --score-min L,4.40237146159707,6.23213280724887 --mp 4.86327024892809,3.11338512861996 -R 3 -k 3 --qseq -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.qseq 743s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 743s parsing sequence Sim.pm.1... 743s parsing sequence Sim.pm.2... 743s Parsed 166 reference bases 744s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 744s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 744s 61 reads; of these: 744s 61 (100.00%) were unpaired; of these: 744s 61 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s Read 50 alignments... 744s /usr/bin/bowtie2 --local --cp-ival 3 --cp-min 2 --large-index --score-min L,4.40237146159707,6.23213280724887 --mp 4.86327024892809,3.11338512861996 -R 3 -k 3 --qseq -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s --- Summary --- 744s Read 1 reference strings 744s Checked 0 alignments, 0 edits 744s --------------- 744s PASSED 744s ALSO checking that bowtie2 and bowtie2-align match up 744s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 744s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 744s 61 reads; of these: 744s 61 (100.00%) were unpaired; of these: 744s 61 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 744s Flattened IUPAC characters 744s Mutating sequence Sim.pm.2 744s Introducing 4 SNPs, 1/0 ref/read gaps, and 2 rearrangements 744s Finished SNPs 744s *** Run 37 of 100 744s /usr/bin/bowtie2 --trim3 2 --n-ceil 0.736285336354866,0.484162857594827 -a --cp-ival 1 -D 17 --score-min L,8.34354204461029,1.07622162740624 --mm --rdg 10.0058091862564 --np 9 --cp-min 2 --large-index -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 744s Finished ref gaps 744s Finished read gaps 744s Mutating sequence Sim.pm.1 744s Introducing 6 SNPs, 0/3 ref/read gaps, and 0 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutated reference genome to subject genome 744s SNPs introduced: 10 744s Reference gaps introduced: 1 744s Read gaps introduced: 3 744s Rearrangements introduced: 2 744s Created read sampler 744s Sampling 115 reads 744s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 744s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 744s parsing sequence Sim.pm.1... 744s parsing sequence Sim.pm.2... 744s Parsed 166 reference bases 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 744s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '23' because it was < 2 characters long 744s Warning: skipping mate #2 of read '23' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 744s Read 50 alignments... 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 744s Read 100 alignments... 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 744s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '48' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 744s Warning: skipping mate #2 of read '70' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '70' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 744s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '75' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 744s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '76' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 744s Read 150 alignments... 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 744s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '85' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 744s Read 200 alignments... 744s Read 250 alignments... 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 744s Read 300 alignments... 744s 115 reads; of these: 744s 110 (95.65%) were paired; of these: 744s 109 (99.09%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 1 (0.91%) aligned concordantly >1 times 744s ---- 744s 109 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 109 pairs aligned 0 times concordantly or discordantly; of these: 744s 218 mates make up the pairs; of these: 744s 183 (83.94%) aligned 0 times 744s 10 (4.59%) aligned exactly 1 time 744s 25 (11.47%) aligned >1 times 744s 5 (4.35%) were unpaired; of these: 744s 4 (80.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 1 (20.00%) aligned >1 times 744s 16.89% overall alignment rate 744s Read 350 alignments... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GAG 744s GAG 744s Processing line... 744s GAG 744s GAG 744s Processing line... 744s GAG 744s GAG 744s Processing line... 744s GAG 744s GAG 744s Processing line... 744s GAG 744s GAG 744s Processing line... 744s Processing line... 744s CGGGGCGGCGG 744s CGGGGCGGCGG 744s Processing line... 744s CGGGGCGGCGG 744s CGGGGCGGCGG 744s Processing line... 744s CGGGGCGGCGG 744s CGGGGCGGCGG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GAGGGA 744s GAGGGA 744s Processing line... 744s GAGGGA 744s GAGGGA 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s ATGGGCC 744s ATGGGCC 744s Processing line... 744s ATGGGCC 744s ATGGGCC 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GCCGG 744s GCCGG 744s Processing line... 744s GCCGG 744s GCCGG 744s Processing line... 744s GCCGG 744s GCCGG 744s Processing line... 744s Processing line... 744s GGCGGTTGCTTTAGGAGGGA 744s GGCGGTTGCTTTAGGAGGGA 744s Processing line... 744s GGCGGTTGCTTTAGGAGGGA 744s GGCGGTTGCTTTAGGAGGGA 744s Processing line... 744s Processing line... 744s TAGGAGGGATGGGCCGGGGC 744s TAGGAGGGATGGGCCGGGGC 744s Processing line... 744s TAGGAGGGATGGGCCGGGGC 744s TAGGAGGGATGGGCCGGGGC 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s TTGA 744s TTGA 744s Processing line... 744s TTGA 744s TTGA 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s TTGTAGTGGCGGTC 744s TTGTAGTGGCGGTC 744s Processing line... 744s Processing line... 744s ACTTTCGGGTGTCATTGT 744s ACTTTCGGGTGTCATTGT 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s ATCGGGAGTGGGCG 744s ATCGGGAGTGGGCG 744s Processing line... 744s Processing line... 744s GCGGCGGTTGCTTTAGGAGGGATGGGC 744s GCGGCGGTTGCTTTAGGAGGGATGGGC 744s Processing line... 744s GCGGCGGTTGCTTTAGGAGGGATGGGC 744s GCGGCGGTTGCTTTAGGAGGGATGGGC 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GCGG 744s GCGG 744s Processing line... 744s GCGG 744s GCGG 744s Processing line... 744s GCGG 744s GCGG 744s Processing line... 744s GCGG 744s GCGG 744s Processing line... 744s GCGG 744s GCGG 744s Processing line... 744s GCGG 744s GCGG 744s Processing line... 744s GCGG 744s GCGG 744s Processing line... 744s GCGG 744s GCGG 744s Processing line... 744s GCGG 744s GCGG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s CT 744s CT 744s Processing line... 744s AG 744s AG 744s Processing line... 744s AG 744s AG 744s Processing line... 744s AG 744s AG 744s Processing line... 744s AG 744s AG 744s Processing line... 744s CT 744s CT 744s Processing line... 744s AG 744s AG 744s Processing line... 744s AG 744s AG 744s Processing line... 744s AG 744s AG 744s Processing line... 744s CT 744s CT 744s Processing line... 744s CT 744s CT 744s Processing line... 744s AG 744s AG 744s Processing line... 744s CT 744s CT 744s Processing line... 744s CT 744s CT 744s Processing line... 744s AG 744s AG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s AGG 744s AGG 744s Processing line... 744s AGG 744s AGG 744s Processing line... 744s AGG 744s AGG 744s Processing line... 744s AGG 744s AGG 744s Processing line... 744s AGG 744s AGG 744s Processing line... 744s AGG 744s AGG 744s Processing line... 744s AGG 744s AGG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s CGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGG 744s CGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGG 744s Processing line... 744s CGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGG 744s CGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGG 744s Processing line... 744s Processing line... 744s TGGGCCGGGGCGGCGGTTGCTTTAGGAGGGA 744s TGGGCCGGGGCGGCGGTTGCTTTAGGAGGGA 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GGCGGTTGCTTT 744s GGCGGTTGCTTT 744s Processing line... 744s GGCGGTTGCTTT 744s GGCGGTTGCTTT 744s Processing line... 744s GGCGGTTGCTTT 744s GGCGGTTGCTTT 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GGTG 744s GGTG 744s Processing line... 744s Processing line... 744s TCGGGTGTCATTGTAGTGGC 744s TCGGGTGTCATTGTAGTGGC 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GGTTGACTTTCGGG 744s GGTTGACTTTCGGG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GCTTTAGGAGGGATGGGCCGG 744s GCTTTAGGAGGGATGGGCCGG 744s Processing line... 744s GCTTTAGGAGGGATGGGCCGG 744s GCTTTAGGAGGGATGGGCCGG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s CGGGAGTGGGCGGTTGACT 744s CGGGAGTGGGCGGTTGACT 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GGCGG 744s GGCGG 744s Processing line... 744s GGCGG 744s GGCGG 744s Processing line... 744s GGCGG 744s GGCGG 744s Processing line... 744s GGCGG 744s GGCGG 744s Processing line... 744s GGCGG 744s GGCGG 744s Processing line... 744s GGCGG 744s GGCGG 744s Processing line... 744s GGCGG 744s GGCGG 744s Processing line... 744s GGCGG 744s GGCGG 744s Processing line... 744s GGCGG 744s GGCGG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s ATGGGCCGGGGCGGC 744s ATGGGCCGGGGCGGC 744s Processing line... 744s AGGGATGGGCCGGGGCGGCGGT 744s AGGGATGGGCCGGGGCGGCGGT 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s GGG 744s GGG 744s Processing line... 744s Processing line... 744s GCG 744s GCG 744s Processing line... 744s GCG 744s GCG 744s Processing line... 744s GCG 744s GCG 744s Processing line... 744s GCG 744s GCG 744s Processing line... 744s GCG 744s GCG 744s Processing line... 744s GCG 744s GCG 744s Processing line... 744s GCG 744s GCG 744s Processing line... 744s GCG 744s GCG 744s Processing line... 744s GCG 744s GCG 744s Processing line... 744s GCG 744s GCG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GGCGGTTG 744s GGCGGTTG 744s Processing line... 744s GGCGGTTG 744s GGCGGTTG 744s Processing line... 744s GGCGGTTG 744s GGCGGTTG 744s Processing line... 744s GGCGGTTG 744s GGCGGTTG 744s Processing line... 744s GGCGGTTG 744s GGCGGTTG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s TGCTTTAGG 744s TGCTTTAGG 744s Processing line... 744s TGCTTTAGG 744s TGCTTTAGG 744s Processing line... 744s TGCTTTAGG 744s TGCTTTAGG 744s Processing line... 744s GTCTGAG 744s GTCTGAG 744s Processing line... 744s AGGG 744s AGGG 744s Processing line... 744s AGGG 744s AGGG 744s Processing line... 744s AGGG 744s AGGG 744s Processing line... 744s Processing line... 744s TCG 744s TCG 744s Processing line... 744s TCG 744s TCG 744s Processing line... 744s TCG 744s TCG 744s Processing line... 744s CGA 744s CGA 744s Processing line... 744s GGGCCGGGGCGGCGGTTGCTTTAGGA 744s GGGCCGGGGCGGCGGTTGCTTTAGGA 744s Processing line... 744s GGGCCGGGGCGGCGGTTGCTTTAGGA 744s GGGCCGGGGCGGCGGTTGCTTTAGGA 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s CCGGGGCGGCGGTTGCT 744s CCGGGGCGGCGGTTGCT 744s Processing line... 744s CCGGGGCGGCGGTTGCT 744s CCGGGGCGGCGGTTGCT 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s CATTGTAGTGGCGGTCTGAGG 744s CATTGTAGTGGCGGTCTGAGG 744s Processing line... 744s --- Summary --- 744s Read 1 reference strings 744s Checked 192 alignments, 0 edits 744s --------------- 744s PASSED 744s ALSO checking that bowtie2 and bowtie2-align match up 744s /usr/bin/bowtie2 --trim3 2 --n-ceil 0.736285336354866,0.484162857594827 -a --cp-ival 1 -D 17 --score-min L,8.34354204461029,1.07622162740624 --mm --rdg 10.0058091862564 --np 9 --cp-min 2 --large-index -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 744s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '23' because it was < 2 characters long 744s Warning: skipping mate #2 of read '23' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 744s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '48' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 744s Warning: skipping mate #2 of read '70' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '70' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 744s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '75' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 744s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '76' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 744s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '85' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 744s 115 reads; of these: 744s 110 (95.65%) were paired; of these: 744s 109 (99.09%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 1 (0.91%) aligned concordantly >1 times 744s ---- 744s 109 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 109 pairs aligned 0 times concordantly or discordantly; of these: 744s 218 mates make up the pairs; of these: 744s 183 (83.94%) aligned 0 times 744s 10 (4.59%) aligned exactly 1 time 744s 25 (11.47%) aligned >1 times 744s 5 (4.35%) were unpaired; of these: 744s 4 (80.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 1 (20.00%) aligned >1 times 744s 16.89% overall alignment rate 744s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 744s Flattened IUPAC characters 744s Mutating sequence Sim.pm.1 744s Introducing 6 SNPs, 1/2 ref/read gaps, and 2 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutating sequence Sim.pm.2 744s Introducing 13 SNPs, 0/1 ref/read gaps, and 1 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutated reference genome to subject genome 744s SNPs introduced: 19 744s Reference gaps introduced: 1 744s Read gaps introduced: 3 744s Rearrangements introduced: 3 744s Created read sampler 744s Sampling 158 reads 744s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 744s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 744s parsing sequence Sim.pm.1... 744s parsing sequence Sim.pm.2... 744s Parsed 166 reference bases 744s *** Run 38 of 100 744s /usr/bin/bowtie2 --np 2 --cp-min 8 --large-index -R 1 -k 4 --score-min L,9.04541327378719,7.54484524964907 --cp-ival 3 --local --norc --trim3 7 --nofw -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 744s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '3' because it was < 2 characters long 744s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '9' because it was < 2 characters long 744s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '15' because it was < 2 characters long 744s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '23' because it was < 2 characters long 744s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '24' because it was < 2 characters long 744s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '32' because it was < 2 characters long 744s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '37' because it was < 2 characters long 744s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '42' because it was < 2 characters long 744s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '44' because it was < 2 characters long 744s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '48' because it was < 2 characters long 744s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '54' because it was < 2 characters long 744s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '55' because it was < 2 characters long 744s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '58' because it was < 2 characters long 744s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '59' because it was < 2 characters long 744s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '60' because it was < 2 characters long 744s Read 50 alignments... 744s Read 100 alignments... 744s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '72' because it was < 2 characters long 744s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '76' because it was < 2 characters long 744s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '80' because it was < 2 characters long 744s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '83' because it was < 2 characters long 744s Warning: skipping mate #1 of read '86' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '86' because it was < 2 characters long 744s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '89' because it was < 2 characters long 744s Warning: skipping read '90' because length (1) <= # seed mismatches (0) 744s Warning: skipping read '90' because it was < 2 characters long 744s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '91' because it was < 2 characters long 744s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '92' because it was < 2 characters long 744s Warning: skipping mate #2 of read '108' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '108' because it was < 2 characters long 744s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '112' because it was < 2 characters long 744s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '119' because it was < 2 characters long 744s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '125' because it was < 2 characters long 744s Read 150 alignments... 744s Warning: skipping mate #1 of read '129' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '129' because it was < 2 characters long 744s Warning: skipping mate #1 of read '139' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '139' because it was < 2 characters long 744s Warning: skipping mate #1 of read '142' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '142' because it was < 2 characters long 744s Read 200 alignments... 744s 158 reads; of these: 744s 138 (87.34%) were paired; of these: 744s 138 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 138 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 138 pairs aligned 0 times concordantly or discordantly; of these: 744s 276 mates make up the pairs; of these: 744s 276 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 20 (12.66%) were unpaired; of these: 744s 20 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s Read 250 alignments... 744s Read 300 alignments... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s 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line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s --- Summary --- 744s Read 1 reference strings 744s Checked 0 alignments, 0 edits 744s --------------- 744s PASSED 744s Flattened IUPAC characters 744s Mutating sequence Sim.pm.1 744s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutating sequence Sim.pm.2 744s Introducing 12 SNPs, 1/0 ref/read gaps, and 1 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutated reference genome to subject genome 744s SNPs introduced: 20 744s Reference gaps introduced: 1 744s Read gaps introduced: 0 744s Rearrangements introduced: 1 744s Created read sampler 744s Sampling 56 reads 744s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 744s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 744s parsing sequence Sim.pm.1... 744s parsing sequence Sim.pm.2... 744s Parsed 166 reference bases 744s *** Run 39 of 100 744s /usr/bin/bowtie2 --score-min L,2.50599973649251,6.54792828884623 --nofw --trim3 6 --gbar 1 -i L,0.0409370220637167 --local --cp-ival 1 --large-index -M 4 --cp-min 3 --trim5 4 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '1' because it was < 2 characters long 744s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '3' because it was < 2 characters long 744s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '4' because it was < 2 characters long 744s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '10' because it was < 2 characters long 744s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '19' because it was < 2 characters long 744s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '36' because it was < 2 characters long 744s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '46' because it was < 2 characters long 744s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '52' because it was < 2 characters long 744s 56 reads; of these: 744s 43 (76.79%) were paired; of these: 744s 43 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 43 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 43 pairs aligned 0 times concordantly or discordantly; of these: 744s 86 mates make up the pairs; of these: 744s 86 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 13 (23.21%) were unpaired; of these: 744s 13 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s Read 50 alignments... 744s Read 100 alignments... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s --- Summary --- 744s Read 1 reference strings 744s Checked 0 alignments, 0 edits 744s --------------- 744s PASSED 744s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 744s /usr/bin/bowtie2 --score-min L,2.50599973649251,6.54792828884623 --nofw --trim3 6 --gbar 1 -i L,0.0409370220637167 --local --cp-ival 1 --large-index -M 4 --cp-min 3 --trim5 4 -r -p 4 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '1' because it was < 2 characters long 744s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '3' because it was < 2 characters long 744s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '4' because it was < 2 characters long 744s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '10' because it was < 2 characters long 744s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '19' because it was < 2 characters long 744s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '36' because it was < 2 characters long 744s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '46' because it was < 2 characters long 744s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '52' because it was < 2 characters long 744s 56 reads; of these: 744s 43 (76.79%) were paired; of these: 744s 43 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 43 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 43 pairs aligned 0 times concordantly or discordantly; of these: 744s 86 mates make up the pairs; of these: 744s 86 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 13 (23.21%) were unpaired; of these: 744s 13 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 744s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 744s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 744s /usr/bin/bowtie2 --score-min L,2.50599973649251,6.54792828884623 --nofw --trim3 6 --gbar 1 -i L,0.0409370220637167 --local --cp-ival 1 --large-index -M 4 --cp-min 3 --trim5 4 -r -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 744s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '1' because it was < 2 characters long 744s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '3' because it was < 2 characters long 744s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '4' because it was < 2 characters long 744s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '10' because it was < 2 characters long 744s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '19' because it was < 2 characters long 744s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '36' because it was < 2 characters long 744s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '46' because it was < 2 characters long 744s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '52' because it was < 2 characters long 744s 56 reads; of these: 744s 43 (76.79%) were paired; of these: 744s 43 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 43 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 43 pairs aligned 0 times concordantly or discordantly; of these: 744s 86 mates make up the pairs; of these: 744s 86 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 13 (23.21%) were unpaired; of these: 744s 13 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 744s Flattened IUPAC characters 744s Mutating sequence Sim.pm.1 744s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutating sequence Sim.pm.2 744s Introducing 7 SNPs, 0/3 ref/read gaps, and 0 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutated reference genome to subject genome 744s SNPs introduced: 11 744s Reference gaps introduced: 0 744s Read gaps introduced: 3 744s Rearrangements introduced: 0 744s Created read sampler 744s Sampling 67 reads 744s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 744s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 744s parsing sequence Sim.pm.1... 744s parsing sequence Sim.pm.2... 744s Parsed 166 reference bases 744s *** Run 40 of 100 744s /usr/bin/bowtie2 --trim3 0 --mp 7.83441411979739,5.72794785018804 -M 3 --norc --local --cp-ival 1 --score-min L,3.80188215065747,2.01102689371318 --rdg 29.208248158312,11.403749853521 --mm --cp-min 12 --np 9 --large-index --qseq -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.qseq 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 744s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 744s 67 reads; of these: 744s 67 (100.00%) were unpaired; of these: 744s 67 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s Read 50 alignments... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s /usr/bin/bowtie2 --trim3 0 --mp 7.83441411979739,5.72794785018804 -M 3 --norc --local --cp-ival 1 --score-min L,3.80188215065747,2.01102689371318 --rdg 29.208248158312,11.403749853521 --mm --cp-min 12 --np 9 --large-index --qseq -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s --- Summary --- 744s Read 1 reference strings 744s Checked 0 alignments, 0 edits 744s --------------- 744s PASSED 744s ALSO checking that bowtie2 and bowtie2-align match up 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 744s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 744s 67 reads; of these: 744s 67 (100.00%) were unpaired; of these: 744s 67 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 744s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 744s /usr/bin/bowtie2 --trim3 0 --mp 7.83441411979739,5.72794785018804 -M 3 --norc --local --cp-ival 1 --score-min L,3.80188215065747,2.01102689371318 --rdg 29.208248158312,11.403749853521 --mm --cp-min 12 --np 9 --large-index --qseq -p 2 -x /tmp/Sim.pm.pBDT5Pxz --reorder /tmp/Sim.pm.pBDT5Pxz_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 745s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 745s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 745s 67 reads; of these: 745s 67 (100.00%) were unpaired; of these: 745s 67 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 0.00% overall alignment rate 745s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 745s Flattened IUPAC characters 745s Mutating sequence Sim.pm.2 745s Introducing 6 SNPs, 1/2 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutating sequence Sim.pm.1 745s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutated reference genome to subject genome 745s SNPs introduced: 14 745s Reference gaps introduced: 1 745s Read gaps introduced: 3 745s Rearrangements introduced: 0 745s Created read sampler 745s Sampling 100 reads 745s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 745s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 745s parsing sequence Sim.pm.1... 745s parsing sequence Sim.pm.2... 745s Parsed 166 reference bases 745s *** Run 41 of 100 745s /usr/bin/bowtie2 --rfg 21.6424402262119 -k 2 --trim3 2 --ma 27.0146173179347 --score-min L,3.67595271321758,6.61435585898359 --cp-ival 1 --cp-min 13 --large-index -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq 745s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 745s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 745s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '10' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 745s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '28' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 745s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '31' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 745s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '47' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 745s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '48' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 745s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '58' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 745s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '68' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 745s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '79' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 745s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '91' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 745s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '96' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 745s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '100' because it was < 2 characters long 745s 100 reads; of these: 745s 100 (100.00%) were unpaired; of these: 745s 80 (80.00%) aligned 0 times 745s 3 (3.00%) aligned exactly 1 time 745s 17 (17.00%) aligned >1 times 745s 20.00% overall alignment rate 745s Read 50 alignments... 745s Read 100 alignments... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GG 745s GG 745s Processing line... 745s GG 745s GG 745s Processing line... 745s CTG 745s CTG 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GCGG 745s GCGG 745s Processing line... 745s GCGG 745s GCGG 745s Processing line... 745s Processing line... 745s Processing line... 745s TCTGAGGCCG 745s TCTGAGGCCG 745s Processing line... 745s AGGGATGGG 745s AGGGATGGG 745s Processing line... 745s AGGGATGGG 745s AGGGATGGG 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s AG 745s AG 745s Processing line... 745s AG 745s AG 745s Processing line... 745s GGGGCGG 745s GGGGCGG 745s Processing line... 745s GGGGCGG 745s GGGGCGG 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TGAC 745s TGAC 745s Processing line... 745s TGAC 745s TGAC 745s Processing line... 745s GGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGC 745s GGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGC 745s Processing line... 745s /usr/bin/bowtie2 --rfg 21.6424402262119 -k 2 --trim3 2 --ma 27.0146173179347 --score-min L,3.67595271321758,6.61435585898359 --cp-ival 1 --cp-min 13 --large-index -q -p 4 -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 745s GGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGC 745s GGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGC 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GGGG 745s GGGG 745s Processing line... 745s GGGG 745s GGGG 745s Processing line... 745s Processing line... 745s CGGTC 745s CGGTC 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GGCGGCGGTTGCTTTAGGAGGGATGGG 745s GGCGGCGGTTGCTTTAGGAGGGATGGG 745s Processing line... 745s GGCGGCGGTTGCTTTAGGAGGGATGGG 745s GGCGGCGGTTGCTTTAGGAGGGATGGG 745s Processing line... 745s Processing line... 745s TTGCTTTAG 745s TTGCTTTAG 745s Processing line... 745s TTGCTTTAG 745s TTGCTTTAG 745s Processing line... 745s Processing line... 745s TGA 745s TGA 745s Processing line... 745s TGA 745s TGA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GA 745s GA 745s Processing line... 745s GA 745s GA 745s Processing line... 745s GGGATGGGCCGGGGCGGCGGTTGCTT 745s GGGATGGGCCGGGGCGGCGGTTGCTT 745s Processing line... 745s GGGATGGGCCGGGGCGGCGGTTGCTT 745s GGGATGGGCCGGGGCGGCGGTTGCTT 745s Processing line... 745s Processing line... 745s Processing line... 745s TGGGCCGGGGCGGCGGTTGC 745s TGGGCCGGGGCGGCGGTTGC 745s Processing line... 745s TGGGCCGGGGCGGCGGTTGC 745s TGGGCCGGGGCGGCGGTTGC 745s Processing line... 745s Processing line... 745s Processing line... 745s TT 745s TT 745s Processing line... 745s TT 745s TT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GGCCGGGGCGG 745s GGCCGGGGCGG 745s Processing line... 745s GGCCGGGGCGG 745s GGCCGGGGCGG 745s Processing line... 745s CT 745s CT 745s Processing line... 745s CT 745s CT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s --- Summary --- 745s Read 1 reference strings 745s Checked 37 alignments, 0 edits 745s --------------- 745s PASSED 745s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 745s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 745s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 745s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '10' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 745s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '28' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 745s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '31' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 745s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '47' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 745s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '48' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 745s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '58' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 745s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '68' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 745s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '79' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 745s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '91' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 745s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '96' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 745s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '100' because it was < 2 characters long 745s 100 reads; of these: 745s 100 (100.00%) were unpaired; of these: 745s 80 (80.00%) aligned 0 times 745s 3 (3.00%) aligned exactly 1 time 745s 17 (17.00%) aligned >1 times 745s 20.00% overall alignment rate 745s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 745s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 745s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 745s /usr/bin/bowtie2 --rfg 21.6424402262119 -k 2 --trim3 2 --ma 27.0146173179347 --score-min L,3.67595271321758,6.61435585898359 --cp-ival 1 --cp-min 13 --large-index -q -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder /tmp/Sim.pm.pBDT5Pxz_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 745s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 745s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 745s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 745s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '10' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 745s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '28' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 745s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '31' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 745s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '47' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 745s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '48' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 745s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '58' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 745s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '68' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 745s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '79' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 745s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '91' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 745s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '96' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 745s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '100' because it was < 2 characters long 745s 100 reads; of these: 745s 100 (100.00%) were unpaired; of these: 745s 80 (80.00%) aligned 0 times 745s 3 (3.00%) aligned exactly 1 time 745s 17 (17.00%) aligned >1 times 745s 20.00% overall alignment rate 745s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 745s *** Run 42 of 100 745s /usr/bin/bowtie2 --cp-ival 1 --local --n-ceil 0.774302376814048,1.39712334668985 -a --rfg 21.3187097507018,13.4766129350812 --cp-min 14 --np 5 --large-index --mm -R 3 --score-min L,2.42343247169245,8.88663816143025 --qseq -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.qseq 745s Flattened IUPAC characters 745s Mutating sequence Sim.pm.1 745s Introducing 9 SNPs, 2/0 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutating sequence Sim.pm.2 745s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutated reference genome to subject genome 745s SNPs introduced: 14 745s Reference gaps introduced: 3 745s Read gaps introduced: 0 745s Rearrangements introduced: 0 745s Created read sampler 745s Sampling 105 reads 745s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 745s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 745s parsing sequence Sim.pm.1... 745s parsing sequence Sim.pm.2... 745s Parsed 166 reference bases 745s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 745s 105 reads; of these: 745s 105 (100.00%) were unpaired; of these: 745s 105 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 0.00% overall alignment rate 745s Read 50 alignments... 745s Read 100 alignments... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s --- Summary --- 745s Read 1 reference strings 745s Checked 0 alignments, 0 edits 745s --------------- 745s PASSED 745s Flattened IUPAC characters 745s Mutating sequence Sim.pm.1 745s Introducing 11 SNPs, 2/1 ref/read gaps, and 1 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutating sequence Sim.pm.2 745s Introducing 2 SNPs, 0/2 ref/read gaps, and 1 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutated reference genome to subject genome 745s SNPs introduced: 13 745s Reference gaps introduced: 2 745s Read gaps introduced: 3 745s Rearrangements introduced: 2 745s Created read sampler 745s Sampling 17 reads 745s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 745s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 745s parsing sequence Sim.pm.1... 745s parsing sequence Sim.pm.2... 745s Parsed 166 reference bases 745s *** Run 43 of 100 745s /usr/bin/bowtie2 --rdg 12.9699084313783,12.6062340831989 --mm --ma 5.21378070543118 --score-min L,7.91019627562104,9.49073341335745 --np 2 --cp-min 3 --large-index --rfg 39.2991738330712 --trim3 0 --mp 6.79043551589689,2.94676457134773 --cp-ival 1 --trim5 2 -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq 745s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 745s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 745s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '10' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 745s 17 reads; of these: 745s 17 (100.00%) were unpaired; of these: 745s 15 (88.24%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 2 (11.76%) aligned >1 times 745s 11.76% overall alignment rate 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GAGGGATGGGCCGGGGCGGCGGTTGC 745s GAGGGATGGGCCGGGGCGGCGGTTGC 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s CGGTTGAC 745s CGGTTGAC 745s Processing line... 745s Processing line... 745s Processing line... 745s --- Summary --- 745s Read 1 reference strings 745s Checked 2 alignments, 0 edits 745s /usr/bin/bowtie2 --rdg 12.9699084313783,12.6062340831989 --mm --ma 5.21378070543118 --score-min L,7.91019627562104,9.49073341335745 --np 2 --cp-min 3 --large-index --rfg 39.2991738330712 --trim3 0 --mp 6.79043551589689,2.94676457134773 --cp-ival 1 --trim5 2 -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 745s --------------- 745s PASSED 745s ALSO checking that bowtie2 and bowtie2-align match up 745s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 745s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 745s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '10' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 745s 17 reads; of these: 745s 17 (100.00%) were unpaired; of these: 745s 15 (88.24%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 2 (11.76%) aligned >1 times 745s 11.76% overall alignment ratediff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 745s 745s Flattened IUPAC characters 745s Mutating sequence Sim.pm.2 745s Introducing 16 SNPs, 1/1 ref/read gaps, and 1 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutating sequence Sim.pm.1 745s Introducing 6 SNPs, 1/1 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutated reference genome to subject genome 745s SNPs introduced: 22 745s Reference gaps introduced: 2 745s Read gaps introduced: 2 745s Rearrangements introduced: 1 745s Created read sampler 745s Sampling 51 reads 745s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 745s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 745s parsing sequence Sim.pm.1... 745s parsing sequence Sim.pm.2... 745s Parsed 166 reference bases 745s *** Run 44 of 100 745s /usr/bin/bowtie2 --cp-ival 2 --local --norc -a --rfg 26.5492662967591,9.64241423579176 --trim3 9 --large-index --cp-min 3 --mm --rdg 34.6418214838742 -R 1 --score-min L,7.87537954580377,2.02227984224157 --qseq -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.qseq 745s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 745s 51 reads; of these: 745s 51 (100.00%) were unpaired; of these: 745s 51 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 0.00% overall alignment rate 745s Read 50 alignments... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s --- Summary --- 745s Read 1 reference strings 745s Checked 0 alignments, 0 edits 745s --------------- 745s PASSED 745s Flattened IUPAC characters 745s Mutating sequence Sim.pm.2 745s Introducing 12 SNPs, 2/1 ref/read gaps, and 2 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutating sequence Sim.pm.1 745s Introducing 6 SNPs, 3/1 ref/read gaps, and 1 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutated reference genome to subject genome 745s SNPs introduced: 18 745s Reference gaps introduced: 5 745s Read gaps introduced: 2 745s Rearrangements introduced: 3 745s Created read sampler 745s Sampling 44 reads 745s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 745s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 745s parsing sequence Sim.pm.1... 745s parsing sequence Sim.pm.2... 745s *** Run 45 of 100 745s /usr/bin/bowtie2 --rfg 36.090245098188 --mm --rdg 38.3197889277628 --mp 9.89433776634685,3.39937174084904 --ma 35.0935921720021 --score-min L,9.25420436524198,1.93138921734322 --cp-ival 1 --cp-min 8 --large-index -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 745s Parsed 166 reference bases 745s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 745s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '2' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 745s 44 reads; of these: 745s 44 (100.00%) were paired; of these: 745s 44 (100.00%) aligned concordantly 0 times 745s 0 (0.00%) aligned concordantly exactly 1 time 745s 0 (0.00%) aligned concordantly >1 times 745s ---- 745s 44 pairs aligned concordantly 0 times; of these: 745s 0 (0.00%) aligned discordantly 1 time 745s ---- 745s 44 pairs aligned 0 times concordantly or discordantly; of these: 745s 88 mates make up the pairs; of these: 745s 78 (88.64%) aligned 0 times 745s 2 (2.27%) aligned exactly 1 time 745s 8 (9.09%) aligned >1 times 745s 11.36% overall alignment rate 745s Read 50 alignments... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TTAG 745s TTAG 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GGTTGACT 745s GGTTGACT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GGTC 745s GGTC 745s Processing line... 745s Processing line... 745s GCTTTAGGA 745s GCTTTAGGA 745s Processing line... 745s Processing line... 745s GGTTGACTTTCGGGT 745s GGTTGACTTTCGGGT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s AG 745s AG 745s Processing line... 745s Processing line... 745s TTAG 745s TTAG 745s Processing line... 745s Processing line... 745s GGGATGGGCCGGGGCGGCGGTTGCTTTAG 745s GGGATGGGCCGGGGCGGCGGTTGCTTTAG 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GGGCGGCGGT 745s GGGCGGCGGT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s /usr/bin/bowtie2 --rfg 36.090245098188 --mm --rdg 38.3197889277628 --mp 9.89433776634685,3.39937174084904 --ma 35.0935921720021 --score-min L,9.25420436524198,1.93138921734322 --cp-ival 1 --cp-min 8 --large-index -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s TTGCTTTA 746s TTGCTTTA 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s --- Summary --- 746s Read 1 reference strings 746s Checked 10 alignments, 0 edits 746s --------------- 746s PASSED 746s ALSO checking that bowtie2 and bowtie2-align match up 746s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 746s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '2' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 746s 44 reads; of these: 746s 44 (100.00%) were paired; of these: 746s 44 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 44 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 44 pairs aligned 0 times concordantly or discordantly; of these: 746s 88 mates make up the pairs; of these: 746s 78 (88.64%) aligned 0 times 746s 2 (2.27%) aligned exactly 1 time 746s 8 (9.09%) aligned >1 times 746s 11.36% overall alignment rate 746s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 746s /usr/bin/bowtie2 --rfg 36.090245098188 --mm --rdg 38.3197889277628 --mp 9.89433776634685,3.39937174084904 --ma 35.0935921720021 --score-min L,9.25420436524198,1.93138921734322 --cp-ival 1 --cp-min 8 --large-index -r -p 2 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 746s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 746s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 746s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '2' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 746s 44 reads; of these: 746s 44 (100.00%) were paired; of these: 746s 44 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 44 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 44 pairs aligned 0 times concordantly or discordantly; of these: 746s 88 mates make up the pairs; of these: 746s 78 (88.64%) aligned 0 times 746s 2 (2.27%) aligned exactly 1 time 746s 8 (9.09%) aligned >1 times 746s 11.36% overall alignment rate 746s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 746s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 746s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 746s Flattened IUPAC characters 746s Mutating sequence Sim.pm.1 746s Introducing 7 SNPs, 3/2 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutating sequence Sim.pm.2 746s Introducing 9 SNPs, 1/3 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutated reference genome to subject genome 746s SNPs introduced: 16 746s Reference gaps introduced: 4 746s Read gaps introduced: 5 746s Rearrangements introduced: 0 746s Created read sampler 746s Sampling 101 reads 746s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 746s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 746s *** Run 46 of 100 746s /usr/bin/bowtie2 --trim3 0 --mp 7.02129136482709,1.33731616552541 -a --norc --n-ceil 0.486745243833096,0.213614114167727 --local --cp-ival 1 --score-min L,3.47712894974088,2.45272605097001 -D 48 --rdg 41.909128805751,7.62629022460183 --large-index --np 1 --cp-min 4 -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq 746s parsing sequence Sim.pm.1... 746s parsing sequence Sim.pm.2... 746s Parsed 166 reference bases 746s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '17' because it was < 2 characters long 746s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '57' because it was < 2 characters long 746s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '62' because it was < 2 characters long 746s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '76' because it was < 2 characters long 746s 101 reads; of these: 746s 101 (100.00%) were unpaired; of these: 746s 101 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 0.00% overall alignment rate 746s Read 50 alignments... 746s Read 100 alignments... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s /usr/bin/bowtie2 --trim3 0 --mp 7.02129136482709,1.33731616552541 -a --norc --n-ceil 0.486745243833096,0.213614114167727 --local --cp-ival 1 --score-min L,3.47712894974088,2.45272605097001 -D 48 --rdg 41.909128805751,7.62629022460183 --large-index --np 1 --cp-min 4 -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s --- Summary --- 746s Read 1 reference strings 746s Checked 0 alignments, 0 edits 746s --------------- 746s PASSED 746s ALSO checking that bowtie2 and bowtie2-align match up 746s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '17' because it was < 2 characters long 746s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '57' because it was < 2 characters long 746s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '62' because it was < 2 characters long 746s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '76' because it was < 2 characters long 746s 101 reads; of these: 746s 101 (100.00%) were unpaired; of these: 746s 101 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 0.00% overall alignment rate 746s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 746s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 746s /usr/bin/bowtie2 --trim3 0 --mp 7.02129136482709,1.33731616552541 -a --norc --n-ceil 0.486745243833096,0.213614114167727 --local --cp-ival 1 --score-min L,3.47712894974088,2.45272605097001 -D 48 --rdg 41.909128805751,7.62629022460183 --large-index --np 1 --cp-min 4 -q -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder /tmp/Sim.pm.pBDT5Pxz_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 746s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '17' because it was < 2 characters long 746s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '57' because it was < 2 characters long 746s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '62' because it was < 2 characters long 746s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '76' because it was < 2 characters long 746s 101 reads; of these: 746s 101 (100.00%) were unpaired; of these: 746s 101 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 0.00% overall alignment rate 746s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 746s Flattened IUPAC characters 746s Mutating sequence Sim.pm.1 746s Introducing 16 SNPs, 1/1 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutating sequence Sim.pm.2 746s Introducing 23 SNPs, 0/1 ref/read gaps, and 1 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutated reference genome to subject genome 746s SNPs introduced: 39 746s Reference gaps introduced: 1 746s Read gaps introduced: 2 746s Rearrangements introduced: 1 746s Created read sampler 746s Sampling 172 reads 746s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 746s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 746s parsing sequence Sim.pm.1... 746s parsing sequence Sim.pm.2... 746s *** Run 47 of 100 746s /usr/bin/bowtie2 --local --cp-ival 1 -M 2 --norc --n-ceil 1.17817876867261,1.3476884479418 --rfg 38.6741633365415 --large-index --cp-min 11 --np 8 --rdg 27.6721957186873,18.9555832488577 --score-min L,8.22806997894587,2.92901582781521 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 746s Parsed 166 reference bases 746s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 746s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '16' because it was < 2 characters long 746s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '19' because it was < 2 characters long 746s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '34' because it was < 2 characters long 746s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '47' because it was < 2 characters long 746s Warning: skipping mate #1 of read '60' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '60' because it was < 2 characters long 746s Read 50 alignments... 746s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '89' because it was < 2 characters long 746s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '99' because it was < 2 characters long 746s Warning: skipping mate #1 of read '109' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '109' because it was < 2 characters long 746s Warning: skipping mate #1 of read '111' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '111' because it was < 2 characters long 746s Warning: skipping mate #1 of read '118' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '118' because it was < 2 characters long 746s Warning: skipping mate #2 of read '120' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '120' because it was < 2 characters long 746s Warning: skipping mate #1 of read '121' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '121' because it was < 2 characters long 746s Warning: skipping mate #2 of read '130' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '130' because it was < 2 characters long 746s Warning: skipping mate #1 of read '137' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '137' because it was < 2 characters long 746s Warning: skipping mate #1 of read '146' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '146' because it was < 2 characters long 746s Read 100 alignments... 746s Read 150 alignments... 746s Read 200 alignments... 746s Read 250 alignments... 746s 172 reads; of these: 746s 172 (100.00%) were paired; of these: 746s 172 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 172 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 172 pairs aligned 0 times concordantly or discordantly; of these: 746s 344 mates make up the pairs; of these: 746s 344 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 0.00% overall alignment rate 746s Read 300 alignments... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 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line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s 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line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s --- Summary --- 746s Read 1 reference strings 746s Checked 0 alignments, 0 edits 746s --------------- 746s PASSED 746s Flattened IUPAC characters 746s Mutating sequence Sim.pm.1 746s Introducing 8 SNPs, 0/2 ref/read gaps, and 1 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutating sequence Sim.pm.2 746s Introducing 12 SNPs, 1/0 ref/read gaps, and 3 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutated reference genome to subject genome 746s SNPs introduced: 20 746s Reference gaps introduced: 1 746s Read gaps introduced: 2 746s Rearrangements introduced: 4 746s Created read sampler 746s Sampling 125 reads 746s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 746s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 746s parsing sequence Sim.pm.1... 746s parsing sequence Sim.pm.2... 746s Parsed 166 reference bases 746s *** Run 48 of 100 746s /usr/bin/bowtie2 --score-min L,5.86099658309701,2.53183483761082 --mp 7.79744665640545,4.26539330908956 --rdg 30.5817326639999 --mm --rfg 34.6947171548619 --large-index --cp-min 2 --norc --cp-ival 1 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 746s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '7' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 746s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '31' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 746s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '33' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 746s Warning: skipping mate #2 of read '68' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '68' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 746s Warning: skipping mate #1 of read '98' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '98' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 746s Warning: skipping mate #2 of read '124' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '124' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 746s Read 50 alignments... 746s Read 100 alignments... 746s 125 reads; of these: 746s 125 (100.00%) were paired; of these: 746s 124 (99.20%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 1 (0.80%) aligned concordantly >1 times 746s ---- 746s 124 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 124 pairs aligned 0 times concordantly or discordantly; of these: 746s 248 mates make up the pairs; of these: 746s 228 (91.94%) aligned 0 times 746s 5 (2.02%) aligned exactly 1 time 746s 15 (6.05%) aligned >1 times 746s 8.80% overall alignment rate 746s Read 150 alignments... 746s Read 200 alignments... 746s Read 250 alignments... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GGCGGCGGTTGCTTTA 746s GGCGGCGGTTGCTTTA 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GGA 746s GGA 746s Processing line... 746s Processing line... 746s TTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGC 746s TTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGC 746s Processing line... 746s Processing line... 746s TT 746s TT 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GA 746s GA 746s Processing line... 746s Processing line... 746s GC 746s GC 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GTC 746s GTC 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GGC 746s GGC 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s TG 746s TG 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s CA 746s CA 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s AGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGG 746s AGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGG 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s CTG 746s CTG 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s CGGGGCGGCGGTTGCTTTA 746s CGGGGCGGCGGTTGCTTTA 746s Processing line... 746s Processing line... 746s TTGCTT 746s TTGCTT 746s Processing line... 746s TGCTTTAGGAGGGAT 746s TGCTTTAGGAGGGAT 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s TGA 746s TGA 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GG 746s GG 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s CGGG 746s CGGG 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GCTTTAGGA 746s GCTTTAGGA 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s CG 746s CG 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s CTTTAGGAGGGATGGGCCGGGGCGGCGGTTG 746s CTTTAGGAGGGATGGGCCGGGGCGGCGGTTG 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s TTTCGGGTGTCATTGTAG 746s TTTCGGGTGTCATTGTAG 746s Processing line... 746s --- Summary --- 746s Read 1 reference strings 746s Checked 22 alignments, 0 edits 746s /usr/bin/bowtie2 --score-min L,5.86099658309701,2.53183483761082 --mp 7.79744665640545,4.26539330908956 --rdg 30.5817326639999 --mm --rfg 34.6947171548619 --large-index --cp-min 2 --norc --cp-ival 1 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 746s --------------- 746s PASSED 746s ALSO checking that bowtie2 and bowtie2-align match up 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 746s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '7' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 746s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '31' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 746s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '33' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 746s Warning: skipping mate #2 of read '68' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '68' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 746s Warning: skipping mate #1 of read '98' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '98' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 746s Warning: skipping mate #2 of read '124' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '124' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 746s 125 reads; of these: 746s 125 (100.00%) were paired; of these: 746s 124 (99.20%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 1 (0.80%) aligned concordantly >1 times 746s ---- 746s 124 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 124 pairs aligned 0 times concordantly or discordantly; of these: 746s 248 mates make up the pairs; of these: 746s 228 (91.94%) aligned 0 times 746s 5 (2.02%) aligned exactly 1 time 746s 15 (6.05%) aligned >1 times 746s 8.80% overall alignment rate 746s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 746s /usr/bin/bowtie2 --score-min L,5.86099658309701,2.53183483761082 --mp 7.79744665640545,4.26539330908956 --rdg 30.5817326639999 --mm --rfg 34.6947171548619 --large-index --cp-min 2 --norc --cp-ival 1 -f -p 2 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 746s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 747s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '7' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 747s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read '33' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 747s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read '31' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 747s Warning: skipping mate #2 of read '68' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read '68' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 747s Warning: skipping mate #1 of read '98' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '98' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 747s Warning: skipping mate #2 of read '124' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read '124' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 747s 125 reads; of these: 747s 125 (100.00%) were paired; of these: 747s 124 (99.20%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 1 (0.80%) aligned concordantly >1 times 747s ---- 747s 124 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 124 pairs aligned 0 times concordantly or discordantly; of these: 747s 248 mates make up the pairs; of these: 747s 228 (91.94%) aligned 0 times 747s 5 (2.02%) aligned exactly 1 time 747s 15 (6.05%) aligned >1 times 747s 8.80% overall alignment rate 747s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 747s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 747s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 747s Flattened IUPAC characters 747s Mutating sequence Sim.pm.1 747s Introducing 12 SNPs, 1/0 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutating sequence Sim.pm.2 747s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutated reference genome to subject genome 747s SNPs introduced: 20 747s Reference gaps introduced: 1 747s Read gaps introduced: 0 747s Rearrangements introduced: 0 747s Created read sampler 747s Sampling 31 reads 747s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 747s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 747s parsing sequence Sim.pm.1... 747s parsing sequence Sim.pm.2... 747s Parsed 166 reference bases 747s *** Run 49 of 100 747s /usr/bin/bowtie2 --rfg 26.8280642383664,4.57790312316351 --rdg 28.1819509670445,3.04316131988015 -R 2 --score-min L,2.18730076352161,7.90479818727255 --trim3 5 --cp-ival 1 --local --large-index --cp-min 7 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 747s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read '2' because it was < 2 characters long 747s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '3' because it was < 2 characters long 747s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '19' because it was < 2 characters long 747s 31 reads; of these: 747s 29 (93.55%) were paired; of these: 747s 29 (100.00%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 0 (0.00%) aligned concordantly >1 times 747s ---- 747s 29 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 29 pairs aligned 0 times concordantly or discordantly; of these: 747s 58 mates make up the pairs; of these: 747s 58 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 2 (6.45%) were unpaired; of these: 747s 2 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 0.00% overall alignment rate 747s Read 50 alignments... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s /usr/bin/bowtie2 --rfg 26.8280642383664,4.57790312316351 --rdg 28.1819509670445,3.04316131988015 -R 2 --score-min L,2.18730076352161,7.90479818727255 --trim3 5 --cp-ival 1 --local --large-index --cp-min 7 -r -p 2 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s --- Summary --- 747s Read 1 reference strings 747s Checked 0 alignments, 0 edits 747s --------------- 747s PASSED 747s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 747s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read '2' because it was < 2 characters long 747s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '3' because it was < 2 characters long 747s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '19' because it was < 2 characters long 747s 31 reads; of these: 747s 29 (93.55%) were paired; of these: 747s 29 (100.00%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 0 (0.00%) aligned concordantly >1 times 747s ---- 747s 29 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 29 pairs aligned 0 times concordantly or discordantly; of these: 747s 58 mates make up the pairs; of these: 747s 58 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 2 (6.45%) were unpaired; of these: 747s 2 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 0.00% overall alignment rate 747s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 747s Flattened IUPAC characters 747s Mutating sequence Sim.pm.1 747s Introducing 25 SNPs, 0/2 ref/read gaps, and 2 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutating sequence Sim.pm.2 747s Introducing 18 SNPs, 0/0 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutated reference genome to subject genome 747s SNPs introduced: 43 747s Reference gaps introduced: 0 747s Read gaps introduced: 2 747s Rearrangements introduced: 2 747s Created read sampler 747s Sampling 164 reads 747s *** Run 50 of 100 747s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --large-index -M 6 --trim5 3 --rdg 39.9414342185584 --mm --nofw --ma 25.4341198964511 --score-min L,5.98732013763963,9.68037301200987 --gbar 3 -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq 747s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 747s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 747s parsing sequence Sim.pm.1... 747s parsing sequence Sim.pm.2... 747s Parsed 166 reference bases 747s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 747s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 747s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 747s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 747s Warning: skipping read '2' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 747s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '21' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 747s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '22' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 747s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 747s Warning: skipping read '26' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 747s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '53' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 747s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '64' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 747s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '67' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 747s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '73' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 747s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '75' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 747s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '79' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 747s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '96' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 747s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '103' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 747s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '120' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 747s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '127' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 747s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '129' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 747s Read 50 alignments... 747s 164 reads; of these: 747s 164 (100.00%) were unpaired; of these: 747s 150 (91.46%) aligned 0 times 747s 2 (1.22%) aligned exactly 1 time 747s 12 (7.32%) aligned >1 times 747s 8.54% overall alignment rate 747s Read 100 alignments... 747s Read 150 alignments... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s CG 747s CG 747s Processing line... 747s GGGATG 747s GGGATG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s AGGAGGGATGGG 747s AGGAGGGATGGG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GGCGGTTGCTTTAGGAGGGATGGGCCGGG 747s GGCGGTTGCTTTAGGAGGGATGGGCCGGG 747s Processing line... 747s Processing line... 747s Processing line... 747s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --large-index -M 6 --trim5 3 --rdg 39.9414342185584 --mm --nofw --ma 25.4341198964511 --score-min L,5.98732013763963,9.68037301200987 --gbar 3 -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GATGGG 747s GATGGG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GC 747s GC 747s Processing line... 747s Processing line... 747s CG 747s CG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s ATG 747s ATG 747s Processing line... 747s Processing line... 747s GC 747s GC 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TGGGCG 747s TGGGCG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TGACTTTCGGGTGTCATTGTAGTGGCGGTCT 747s TGACTTTCGGGTGTCATTGTAGTGGCGGTCT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TGGC 747s TGGC 747s Processing line... 747s Processing line... 747s Processing line... 747s AG 747s AG 747s Processing line... 747s Processing line... 747s CCG 747s CCG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s --- Summary --- 747s Read 1 reference strings 747s Checked 14 alignments, 0 edits 747s --------------- 747s PASSED 747s ALSO checking that bowtie2 and bowtie2-align match up 747s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 747s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 747s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 747s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 747s Warning: skipping read '2' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 747s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '21' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 747s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '22' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 747s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 747s Warning: skipping read '26' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 747s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '53' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 747s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '64' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 747s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '67' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 747s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '73' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 747s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '75' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 747s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '79' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 747s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '96' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 747s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '103' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 747s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '120' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 747s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '127' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 747s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '129' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 747s 164 reads; of these: 747s 164 (100.00%) were unpaired; of these: 747s 150 (91.46%) aligned 0 times 747s 2 (1.22%) aligned exactly 1 time 747s 12 (7.32%) aligned >1 times 747s 8.54% overall alignment rate 747s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 747s Flattened IUPAC characters 747s Mutating sequence Sim.pm.2 747s Introducing 11 SNPs, 0/2 ref/read gaps, and 1 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutating sequence Sim.pm.1 747s Introducing 14 SNPs, 1/1 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutated reference genome to subject genome 747s SNPs introduced: 25 747s Reference gaps introduced: 1 747s Read gaps introduced: 3 747s Rearrangements introduced: 1 747s Created read sampler 747s Sampling 82 reads 747s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 747s *** Run 51 of 100 747s /usr/bin/bowtie2 --n-ceil 1.41830711092619,0.931473073398327 --large-index --np 10 --cp-min 2 --cp-ival 1 --mp 5.33477669975535,3.27824164305373 -i L,3.04867903475543 --score-min L,4.16060397524915,3.59700328332618 --trim3 9 --rdg 35.4286736135545 --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 747s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 747s parsing sequence Sim.pm.1... 747s parsing sequence Sim.pm.2... 747s Parsed 166 reference bases 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 747s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 747s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 747s Read 50 alignments... 747s Read 100 alignments... 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 747s 82 reads; of these: 747s 66 (80.49%) were paired; of these: 747s 65 (98.48%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 1 (1.52%) aligned concordantly >1 times 747s ---- 747s 65 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 65 pairs aligned 0 times concordantly or discordantly; of these: 747s 130 mates make up the pairs; of these: 747s 113 (86.92%) aligned 0 times 747s 7 (5.38%) aligned exactly 1 time 747s 10 (7.69%) aligned >1 times 747s 16 (19.51%) were unpaired; of these: 747s 13 (81.25%) aligned 0 times 747s 1 (6.25%) aligned exactly 1 time 747s 2 (12.50%) aligned >1 times 747s 14.86% overall alignment rate 747s Read 150 alignments... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GATCG 747s GATCG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GG 747s GG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GCT 747s GCT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s ATCGGGAGTGGGCGGTTGA 747s ATCGGGAGTGGGCGGTTGA 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GGAGGGATG 747s GGAGGGATG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GATGGGCC 747s GATGGGCC 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TTGTAGTGGC 747s TTGTAGTGGC 747s Processing line... 747s Processing line... 747s CCGGGGCGGCGGT 747s CCGGGGCGGCGGT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s AGGAG 747s AGGAG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GATGGGCCGGGGCGGCGGT 747s GATGGGCCGGGGCGGCGGT 747s Processing line... 747s Processing line... 747s GGGAGTGGGCGGTTGACTTTCGGCG 747s GGGAGTGGGCGGTTGACTTTCGGCG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GGGCGGTTGACTTTCGGGT 747s GGGCGGTTGACTTTCGGGT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GG 747s GG 747s Processing line... 747s Processing line... 747s GTT 747s GTT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GGGATGGGCCGGGGCGGCGGTTGC 747s GGGATGGGCCGGGGCGGCGGTTGC 747s Processing line... 747s Processing line... 747s TTAGGAGGGATG 747s TTAGGAGGGATG 747s Processing line... 747s Processing line... 747s AGTGGGCGGT 747s AGTGGGCGGT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TG 747s TG 747s Processing line... 747s CGGTTGACTTTCGGGTGTCATTGTAGTG 747s CGGTTGACTTTCGGGTGTCATTGTAGTG 747s Processing line... 747s Processing line... 747s Processing line... 747s TGGGCG 747s TGGGCG 747s Processing line... 747s TCGGGTGTCATTGT 747s TCGGGTGTCATTGT 747s Processing line... 747s Processing line... 747s /usr/bin/bowtie2 --n-ceil 1.41830711092619,0.931473073398327 --large-index --np 10 --cp-min 2 --cp-ival 1 --mp 5.33477669975535,3.27824164305373 -i L,3.04867903475543 --score-min L,4.16060397524915,3.59700328332618 --trim3 9 --rdg 35.4286736135545 --qseq -p 3 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 747s TGTAGTGGC 747s TGTAGTGGC 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s --- Summary --- 747s Read 1 reference strings 747s Checked 22 alignments, 0 edits 747s --------------- 747s PASSED 747s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 747s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 747s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 747s 82 reads; of these: 747s 66 (80.49%) were paired; of these: 747s 65 (98.48%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 1 (1.52%) aligned concordantly >1 times 747s ---- 747s 65 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 65 pairs aligned 0 times concordantly or discordantly; of these: 747s 130 mates make up the pairs; of these: 747s 113 (86.92%) aligned 0 times 747s 7 (5.38%) aligned exactly 1 time 747s 10 (7.69%) aligned >1 times 747s 16 (19.51%) were unpaired; of these: 747s 13 (81.25%) aligned 0 times 747s 1 (6.25%) aligned exactly 1 time 747s 2 (12.50%) aligned >1 times 747s 14.86% overall alignment rate 747s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 747s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 747s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 747s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 747s /usr/bin/bowtie2 --n-ceil 1.41830711092619,0.931473073398327 --large-index --np 10 --cp-min 2 --cp-ival 1 --mp 5.33477669975535,3.27824164305373 -i L,3.04867903475543 --score-min L,4.16060397524915,3.59700328332618 --trim3 9 --rdg 35.4286736135545 --qseq -p 2 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 747s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 747s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 747s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 747s 82 reads; of these: 747s 66 (80.49%) were paired; of these: 747s 65 (98.48%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 1 (1.52%) aligned concordantly >1 times 747s ---- 747s 65 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 65 pairs aligned 0 times concordantly or discordantly; of these: 747s 130 mates make up the pairs; of these: 747s 113 (86.92%) aligned 0 times 747s 7 (5.38%) aligned exactly 1 time 747s 10 (7.69%) aligned >1 times 747s 16 (19.51%) were unpaired; of these: 747s 13 (81.25%) aligned 0 times 747s 1 (6.25%) aligned exactly 1 time 747s 2 (12.50%) aligned >1 times 747s 14.86% overall alignment rate 747s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 747s Flattened IUPAC characters 747s Mutating sequence Sim.pm.2 747s Introducing 12 SNPs, 0/2 ref/read gaps, and 1 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutating sequence Sim.pm.1 747s Introducing 15 SNPs, 0/0 ref/read gaps, and 2 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutated reference genome to subject genome 747s SNPs introduced: 27 747s Reference gaps introduced: 0 747s Read gaps introduced: 2 747s Rearrangements introduced: 3 747s Created read sampler 747s Sampling 148 reads 747s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 747s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 747s parsing sequence Sim.pm.1... 747s parsing sequence Sim.pm.2... 747s *** Run 52 of 100 747s /usr/bin/bowtie2 --large-index --np 2 --cp-min 9 --mm --score-min L,2.63481432570108,6.70864252105105 --local --cp-ival 1 -a --trim5 3 --rfg 41.894440832095,4.83571821545998 --trim3 6 --mp 9.78718365445296,9.52105120676074 -i S,2.12356892484397 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 747s Parsed 166 reference bases 748s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '4' because it was < 2 characters long 748s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '5' because it was < 2 characters long 748s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '6' because it was < 2 characters long 748s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '10' because it was < 2 characters long 748s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '13' because it was < 2 characters long 748s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '27' because it was < 2 characters long 748s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '29' because it was < 2 characters long 748s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '30' because it was < 2 characters long 748s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '33' because it was < 2 characters long 748s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '35' because it was < 2 characters long 748s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '44' because it was < 2 characters long 748s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '46' because it was < 2 characters long 748s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '64' because it was < 2 characters long 748s Warning: skipping mate #1 of read '69' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '69' because it was < 2 characters long 748s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '75' because it was < 2 characters long 748s Warning: skipping mate #2 of read '75' because it was < 2 characters long 748s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '82' because it was < 2 characters long 748s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '90' because it was < 2 characters long 748s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '94' because it was < 2 characters long 748s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '95' because it was < 2 characters long 748s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '100' because it was < 2 characters long 748s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '108' because it was < 2 characters long 748s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '123' because it was < 2 characters long 748s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '129' because it was < 2 characters long 748s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '133' because it was < 2 characters long 748s Read 50 alignments... 748s Read 100 alignments... 748s Read 150 alignments... 748s Read 200 alignments... 748s 148 reads; of these: 748s 120 (81.08%) were paired; of these: 748s 120 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 120 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 120 pairs aligned 0 times concordantly or discordantly; of these: 748s 240 mates make up the pairs; of these: 748s 240 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 28 (18.92%) were unpaired; of these: 748s 28 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 0.00% overall alignment rate 748s Read 250 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 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line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 0 alignments, 0 edits 748s --------------- 748s PASSED 748s *** Run 53 of 100 748s /usr/bin/bowtie2 --np 6 --cp-min 5 --large-index --mm --score-min L,6.08406608791352,1.15144557779323 -D 17 --local --cp-ival 1 --trim5 3 --rfg 7.73943688015087 --nofw --mp 7.60887909902014,7.40748028067678 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.2 748s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.1 748s Introducing 3 SNPs, 0/2 ref/read gaps, and 1 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 6 748s Reference gaps introduced: 0 748s Read gaps introduced: 2 748s Rearrangements introduced: 1 748s Created read sampler 748s Sampling 34 reads 748s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 748s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 748s parsing sequence Sim.pm.1... 748s parsing sequence Sim.pm.2... 748s Parsed 166 reference bases 748s Warning: skipping mate #1 of read '4' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '4' because it was < 2 characters long 748s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '11' because it was < 2 characters long 748s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '12' because it was < 2 characters long 748s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '26' because it was < 2 characters long 748s 34 reads; of these: 748s 34 (100.00%) were paired; of these: 748s 34 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 34 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 34 pairs aligned 0 times concordantly or discordantly; of these: 748s 68 mates make up the pairs; of these: 748s 64 (94.12%) aligned 0 times 748s 3 (4.41%) aligned exactly 1 time 748s 1 (1.47%) aligned >1 times 748s 5.88% overall alignment rate 748s Read 50 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TGACTTTCGGGTGTCATTGTAGTGGCGGTCTGAGGCCGGATGATC-GG 748s TGACTTTCGGGTGTCATTGTAGTGGCGGTCTGAGGCCGGNTGATCGGG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TCGGGAGTGGGCGGTTGACTTTCG 748s TCGGGAGTGGGCGGTTGACTTTCG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s AGTGGG 748s AGTGGG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GGTTGAC 748s GGTTGAC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 4 alignments, 0 edits 748s --------------- 748s PASSED 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.1 748s Introducing 18 SNPs, 0/0 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.2 748s Introducing 6 SNPs, 2/0 ref/read gaps, and 1 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 24 748s Reference gaps introduced: 2 748s Read gaps introduced: 0 748s Rearrangements introduced: 1 748s Created read sampler 748s Sampling 37 reads 748s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 748s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 748s parsing sequence Sim.pm.1... 748s parsing sequence Sim.pm.2... 748s Parsed 166 reference bases 748s *** Run 54 of 100 748s /usr/bin/bowtie2 -R 2 --score-min L,8.20714252004731,9.58703339188259 --rdg 3.96512520687452,14.9874505912574 --large-index --cp-min 2 --mp 4.03515371446873,1.82600576160964 -N 0 -L30 --nofw --trim3 5 --rfg 21.5329169380935,10.4224449940528 --n-ceil 0.144684967025287,0.834031072395221 --cp-ival 1 --local -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 748s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '3' because it was < 2 characters long 748s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '25' because it was < 2 characters long 748s Warning: skipping mate #2 of read '25' because it was < 2 characters long 748s 37 reads; of these: 748s 31 (83.78%) were paired; of these: 748s 31 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 31 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 31 pairs aligned 0 times concordantly or discordantly; of these: 748s 62 mates make up the pairs; of these: 748s 62 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 6 (16.22%) were unpaired; of these: 748s 6 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 0.00% overall alignment rate 748s Read 50 alignments... 748s Processing line... 748s /usr/bin/bowtie2 -R 2 --score-min L,8.20714252004731,9.58703339188259 --rdg 3.96512520687452,14.9874505912574 --large-index --cp-min 2 --mp 4.03515371446873,1.82600576160964 -N 0 -L30 --nofw --trim3 5 --rfg 21.5329169380935,10.4224449940528 --n-ceil 0.144684967025287,0.834031072395221 --cp-ival 1 --local -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 0 alignments, 0 edits 748s --------------- 748s PASSED 748s ALSO checking that bowtie2 and bowtie2-align match up 748s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '3' because it was < 2 characters long 748s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '25' because it was < 2 characters long 748s Warning: skipping mate #2 of read '25' because it was < 2 characters long 748s 37 reads; of these: 748s 31 (83.78%) were paired; of these: 748s 31 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 31 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 31 pairs aligned 0 times concordantly or discordantly; of these: 748s 62 mates make up the pairs; of these: 748s 62 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 6 (16.22%) were unpaired; of these: 748s 6 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 0.00% overall alignment rate 748s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.1 748s Introducing 1 SNPs, 0/2 ref/read gaps, and 1 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.2 748s Introducing 16 SNPs, 4/0 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 17 748s Reference gaps introduced: 4 748s Read gaps introduced: 2 748s Rearrangements introduced: 1 748s Created read sampler 748s Sampling 121 reads 748s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 748s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 748s parsing sequence Sim.pm.1... 748s parsing sequence Sim.pm.2... 748s *** Run 55 of 100 748s /usr/bin/bowtie2 --large-index --cp-min 7 --np 1 --mm --score-min L,4.86357826711803,2.00585328112241 -R 3 --local --cp-ival 1 --trim5 4 --nofw -i C,3.74748795690782,10.9955238656232 --mp 5.56937444833891,5.07140599706653 --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 748s Parsed 166 reference bases 748s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 748s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 748s Warning: skipping mate #2 of read 'R_1_1_1_103_103_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 748s Read 50 alignments... 748s Read 100 alignments... 748s Read 150 alignments... 748s 121 reads; of these: 748s 111 (91.74%) were paired; of these: 748s 111 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 111 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 111 pairs aligned 0 times concordantly or discordantly; of these: 748s 222 mates make up the pairs; of these: 748s 222 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 10 (8.26%) were unpaired; of these: 748s 10 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 0.00% overall alignment rate 748s Read 200 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing 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line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 0 alignments, 0 edits 748s --------------- 748s PASSED 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.1 748s Introducing 15 SNPs, 0/0 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.2 748s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 15 748s Reference gaps introduced: 1 748s Read gaps introduced: 0 748s Rearrangements introduced: 1 748s Created read sampler 748s Sampling 58 reads 748s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 748s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 748s parsing sequence Sim.pm.1... 748s parsing sequence Sim.pm.2... 748s Parsed 166 reference bases 748s *** Run 56 of 100 748s /usr/bin/bowtie2 -M 9 --n-ceil 0.0114821537751626,0.695022472914732 --local --cp-ival 2 -i L,0.181008742370523 --mp 6.99914547471673,3.64708063472149 --np 4 --cp-min 2 --large-index --score-min L,8.79061492402212,6.2318185990232 -D 41 --rdg 23.6563665018376,8.71812111094608 --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 748s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 748s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 748s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 748s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 748s 58 reads; of these: 748s 58 (100.00%) were paired; of these: 748s 58 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 58 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 58 pairs aligned 0 times concordantly or discordantly; of these: 748s 116 mates make up the pairs; of these: 748s 116 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 0.00% overall alignment rate 748s Read 50 alignments... 748s Read 100 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing 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Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 0 alignments, 0 edits 748s --------------- 748s PASSED 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.1 748s Introducing 7 SNPs, 2/2 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.2 748s Introducing 16 SNPs, 0/2 ref/read gaps, and 1 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 23 748s Reference gaps introduced: 2 748s Read gaps introduced: 4 748s Rearrangements introduced: 1 748s Created read sampler 748s Sampling 200 reads 748s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 748s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 748s parsing sequence Sim.pm.1... 748s *** Run 57 of 100 748s /usr/bin/bowtie2 -D 26 --score-min L,8.97032650582388,2.1925731442723 --mm --large-index --cp-min 8 -i L,0.488869729942608,3.2696597417449 --mp 4.04761961244404,3.64946405412836 --rfg 2.85461468186334,7.24628087502619 -a --cp-ival 1 --local -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 748s parsing sequence Sim.pm.2... 748s Parsed 166 reference bases 748s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '63' because it was < 2 characters long 748s Warning: skipping read '72' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '72' because it was < 2 characters long 748s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '86' because it was < 2 characters long 748s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '89' because it was < 2 characters long 748s Warning: skipping read '133' because length (1) <= # seed mismatches (0) 748s Read 50 alignments... 748s Warning: skipping read '133' because it was < 2 characters long 748s Read 100 alignments... 748s Warning: skipping read '143' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '143' because it was < 2 characters long 748s Warning: skipping read '172' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '172' because it was < 2 characters long 748s 200 reads; of these: 748s 200 (100.00%) were unpaired; of these: 748s 200 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 0.00% overall alignment rate 748s Read 150 alignments... 748s Read 200 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s /usr/bin/bowtie2 -D 26 --score-min L,8.97032650582388,2.1925731442723 --mm --large-index --cp-min 8 -i L,0.488869729942608,3.2696597417449 --mp 4.04761961244404,3.64946405412836 --rfg 2.85461468186334,7.24628087502619 -a --cp-ival 1 --local -r -p 4 -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing 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Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing 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Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 0 alignments, 0 edits 748s --------------- 748s PASSED 748s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 748s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '63' because it was < 2 characters long 748s Warning: skipping read '72' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '72' because it was < 2 characters long 748s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '86' because it was < 2 characters long 748s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '89' because it was < 2 characters long 748s Warning: skipping read '133' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '133' because it was < 2 characters long 748s Warning: skipping read '143' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '143' because it was < 2 characters long 748s Warning: skipping read '172' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '172' because it was < 2 characters long 748s 200 reads; of these: 748s 200 (100.00%) were unpaired; of these: 748s 200 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 0.00% overall alignment rate 748s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 748s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 748s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.1 748s Introducing 17 SNPs, 0/0 ref/read gaps, and 3 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.2 748s Introducing 1 SNPs, 0/3 ref/read gaps, and 1 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 18 748s Reference gaps introduced: 0 748s Read gaps introduced: 3 748s Rearrangements introduced: 4 748s Created read sampler 748s Sampling 65 reads 748s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 748s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 748s parsing sequence Sim.pm.1... 748s parsing sequence Sim.pm.2... 748s Parsed 166 reference bases 748s *** Run 58 of 100 748s /usr/bin/bowtie2 --large-index --cp-min 21 --score-min L,7.88640531121961,6.55262038203549 --gbar 6 -k 12 --rdg 15.0998972577468,4.88985972927794 --norc --n-ceil 0.28190480403691,0.0227796549146393 --local --cp-ival 3 --trim3 9 --nofw --rfg 37.6889851151797 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 748s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '0' because it was < 2 characters long 748s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '1' because it was < 2 characters long 748s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '6' because it was < 2 characters long 748s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '10' because it was < 2 characters long 748s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '11' because it was < 2 characters long 748s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '14' because it was < 2 characters long 748s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '15' because it was < 2 characters long 748s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '16' because it was < 2 characters long 748s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '19' because it was < 2 characters long 748s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '23' because it was < 2 characters long 748s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '31' because it was < 2 characters long 748s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '32' because it was < 2 characters long 748s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '41' because it was < 2 characters long 748s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '43' because it was < 2 characters long 748s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '48' because it was < 2 characters long 748s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '50' because it was < 2 characters long 748s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '53' because it was < 2 characters long 748s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '55' because it was < 2 characters long 748s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '57' because it was < 2 characters long 748s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '62' because it was < 2 characters long 748s 65 reads; of these: 748s 65 (100.00%) were unpaired; of these: 748s 65 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 0.00% overall alignment rate 748s Read 50 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s /usr/bin/bowtie2 --large-index --cp-min 21 --score-min L,7.88640531121961,6.55262038203549 --gbar 6 -k 12 --rdg 15.0998972577468,4.88985972927794 --norc --n-ceil 0.28190480403691,0.0227796549146393 --local --cp-ival 3 --trim3 9 --nofw --rfg 37.6889851151797 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 0 alignments, 0 edits 748s --------------- 748s PASSED 748s ALSO checking that bowtie2 and bowtie2-align match up 748s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '0' because it was < 2 characters long 748s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '1' because it was < 2 characters long 748s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '6' because it was < 2 characters long 748s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '10' because it was < 2 characters long 748s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '11' because it was < 2 characters long 748s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '14' because it was < 2 characters long 748s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '15' because it was < 2 characters long 748s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '16' because it was < 2 characters long 748s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '19' because it was < 2 characters long 748s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '23' because it was < 2 characters long 748s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '31' because it was < 2 characters long 748s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '32' because it was < 2 characters long 748s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '41' because it was < 2 characters long 748s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 748s Warning: skipping read '43' because it was < 2 characters long 748s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '48' because it was < 2 characters long 748s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '50' because it was < 2 characters long 748s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '53' because it was < 2 characters long 748s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '55' because it was < 2 characters long 748s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '57' because it was < 2 characters long 748s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '62' because it was < 2 characters long 748s 65 reads; of these: 748s 65 (100.00%) were unpaired; of these: 748s 65 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 0.00% overall alignment rate 748s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.1 748s Introducing 16 SNPs, 1/1 ref/read gaps, and 2 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.2 748s Introducing 13 SNPs, 0/3 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 29 748s Reference gaps introduced: 1 748s Read gaps introduced: 4 748s Rearrangements introduced: 2 748s Created read sampler 748s Sampling 69 reads 748s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 748s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 748s parsing sequence Sim.pm.1... 748s parsing sequence Sim.pm.2... 748s *** Run 59 of 100 748s /usr/bin/bowtie2 --cp-ival 1 --large-index --cp-min 2 --norc --trim5 1 --score-min L,6.45309368498296,6.14222241243762 --trim3 7 --ma 12.9213248343731 -k 6 -i S,2.04080208412752 --mp 4.77721607036114,2.04157618690933 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 748s Parsed 166 reference bases 748s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 748s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '6' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 748s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '9' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 748s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '12' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 748s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '13' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 748s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '14' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 748s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '20' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 748s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '23' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 748s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '26' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 748s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '27' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 748s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '31' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 748s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '32' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 748s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '43' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 748s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '48' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 748s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '49' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 748s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '59' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 748s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '62' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 748s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '63' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 748s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '64' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 748s Read 50 alignments... 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 748s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '66' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 748s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '68' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '68' because it was < 2 characters long 748s Warning: skipping mate #2 of read '68' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 748s Read 100 alignments... 748s 69 reads; of these: 748s 58 (84.06%) were paired; of these: 748s 58 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 58 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 58 pairs aligned 0 times concordantly or discordantly; of these: 748s 116 mates make up the pairs; of these: 748s 102 (87.93%) aligned 0 times 748s 3 (2.59%) aligned exactly 1 time 748s 11 (9.48%) aligned >1 times 748s 11 (15.94%) were unpaired; of these: 748s 11 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 11.02% overall alignment rate 748s Read 150 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GAGGGA 748s GAGGGA 748s Processing line... 748s GAGGGA 748s GAGGGA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GTAGTGGCGGTCTGAGGCCGG 748s GTAGTGGCGGTCTGAGGCCGG 748s *** Run 60 of 100 748s /usr/bin/bowtie2 -D 36 --gbar 2 --nofw --ma 18.2633679035987 --score-min L,8.122667525628,8.73045063907667 --trim5 2 --cp-min 2 --large-index --cp-ival 3 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GA 748s GA 748s Processing line... 748s GA 748s GA 748s Processing line... 748s GA 748s GA 748s Processing line... 748s GA 748s GA 748s Processing line... 748s GA 748s GA 748s Processing line... 748s GA 748s GA 748s Processing line... 748s Processing line... 748s TG 748s TG 748s Processing line... 748s TG 748s TG 748s Processing line... 748s TG 748s TG 748s Processing line... 748s TG 748s TG 748s Processing line... 748s TG 748s TG 748s Processing line... 748s TG 748s TG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GCC 748s GCC 748s Processing line... 748s GCC 748s GCC 748s Processing line... 748s GCC 748s GCC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TGCTTTAGGAGGGATG 748s TGCTTTAGGAGGGATG 748s Processing line... 748s TGCTTTAGGAGGGATG 748s TGCTTTAGGAGGGATG 748s Processing line... 748s Processing line... 748s GGTGT 748s GGTGT 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GGGGCGGCGGTTGCTTTAGG 748s GGGGCGGCGGTTGCTTTAGG 748s Processing line... 748s GGGGCGGCGGTTGCTTTAGG 748s GGGGCGGCGGTTGCTTTAGG 748s Processing line... 748s GGGGCGGCGGTTGCTTTAGG 748s GGGGCGGCGGTTGCTTTAGG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TCGG 748s TCGG 748s Processing line... 748s TCGG 748s TCGG 748s Processing line... 748s TCGG 748s TCGG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TCGGGAGTGGGC 748s TCGGGAGTGGGC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TTG 748s TTG 748s Processing line... 748s TTG 748s TTG 748s Processing line... 748s TTG 748s TTG 748s Processing line... 748s TTG 748s TTG 748s Processing line... 748s TTG 748s TTG 748s Processing line... 748s TTG 748s TTG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GGGCGG 748s GGGCGG 748s Processing line... 748s GGGCGG 748s GGGCGG 748s Processing line... 748s GGGCGG 748s GGGCGG 748s Processing line... 748s GGGCGG 748s GGGCGG 748s Processing line... 748s GGGCGG 748s GGGCGG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GGGATGGGCCGGGGCGGCGGTTGCTT 748s GGGATGGGCCGGGGCGGCGGTTGCTT 748s Processing line... 748s GGGATGGGCCGGGGCGGCGGTTGCTT 748s GGGATGGGCCGGGGCGGCGGTTGCTT 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CG 748s CG 748s Processing line... 748s CG 748s CG 748s Processing line... 748s CG 748s CG 748s Processing line... 748s CG 748s CG 748s Processing line... 748s CG 748s CG 748s Processing line... 748s CG 748s CG 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 47 alignments, 0 edits 748s --------------- 748s PASSED 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.1 748s Introducing 7 SNPs, 4/1 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.2 748s Introducing 2 SNPs, 0/1 ref/read gaps, and 2 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 9 748s Reference gaps introduced: 4 748s Read gaps introduced: 2 748s Rearrangements introduced: 2 748s Created read sampler 748s Sampling 106 reads 748s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 748s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 748s parsing sequence Sim.pm.1... 748s parsing sequence Sim.pm.2... 748s Parsed 166 reference bases 749s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 749s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '3' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 749s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '36' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 749s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '37' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 749s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '48' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 749s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '56' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 749s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '57' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 749s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '68' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 749s Warning: skipping mate #2 of read '92' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '92' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 749s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '97' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 749s Warning: skipping mate #2 of read '103' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '103' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 749s Read 50 alignments... 749s 106 reads; of these: 749s 101 (95.28%) were paired; of these: 749s 100 (99.01%) aligned concordantly 0 times 749s 0 (0.00%) aligned concordantly exactly 1 time 749s 1 (0.99%) aligned concordantly >1 times 749s ---- 749s 100 pairs aligned concordantly 0 times; of these: 749s 0 (0.00%) aligned discordantly 1 time 749s ---- 749s 100 pairs aligned 0 times concordantly or discordantly; of these: 749s 200 mates make up the pairs; of these: 749s 180 (90.00%) aligned 0 times 749s 7 (3.50%) aligned exactly 1 time 749s 13 (6.50%) aligned >1 times 749s 5 (4.72%) were unpaired; of these: 749s 5 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 10.63% overall alignment rate 749s Read 100 alignments... 749s Read 150 alignments... 749s Read 200 alignments... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s GGGTGTCATTGTAGTGGC 749s GGGTGTCATTGTAGTGGC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TTGTAGTGGCGGTCTGA 749s TTGTAGTGGCGGTCTGA 749s Processing line... 749s Processing line... 749s GCGGTTGACTTTCGGGTGTCATTGTAGTGGCGGTC 749s GCGGTTGACTTTCGGGTGTCATTGTAGTGGCGGTC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CGGG 749s CGGG 749s Processing line... 749s /usr/bin/bowtie2 -D 36 --gbar 2 --nofw --ma 18.2633679035987 --score-min L,8.122667525628,8.73045063907667 --trim5 2 --cp-min 2 --large-index --cp-ival 3 -r -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 749s Processing line... 749s Processing line... 749s Processing line... 749s TGGGCGGTTGACTTTC 749s TGGGCGGTTGACTTTC 749s Processing line... 749s Processing line... 749s GCGGTT 749s GCGGTT 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s ATTG 749s ATTG 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s AGTGG 749s AGTGG 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s GGCGGTC 749s GGCGGTC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TG 749s TG 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TA 749s TA 749s Processing line... 749s Processing line... 749s AC 749s AC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s GG 749s GG 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s GT 749s GT 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s GTAGTGGCGGTCT 749s GTAGTGGCGGTCT 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CGGCGGTTG 749s CGGCGGTTG 749s Processing line... 749s Processing line... 749s GATGGGCCGGGGCGGCGGTTGCT 749s GATGGGCCGGGGCGGCGGTTGCT 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TG 749s TG 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TAGGAGGGATGGGCCGGG 749s TAGGAGGGATGGGCCGGG 749s Processing line... 749s GCG 749s GCG 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TCGGGTGTCATTGTAGTGGCGGTCTGAGGC 749s TCGGGTGTCATTGTAGTGGCGGTCTGAGGC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CCGGGGCGGCGGTTGCTTTAG 749s CCGGGGCGGCGGTTGCTTTAG 749s Processing line... 749s --- Summary --- 749s Read 1 reference strings 749s Checked 22 alignments, 0 edits 749s --------------- 749s PASSED 749s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 749s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 749s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '3' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 749s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '36' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 749s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '37' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 749s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '48' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 749s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '56' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 749s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '57' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 749s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '68' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 749s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '97' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 749s Warning: skipping mate #2 of read '103' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '103' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 749s Warning: skipping mate #2 of read '92' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '92' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 749s 106 reads; of these: 749s 101 (95.28%) were paired; of these: 749s 100 (99.01%) aligned concordantly 0 times 749s 0 (0.00%) aligned concordantly exactly 1 time 749s 1 (0.99%) aligned concordantly >1 times 749s ---- 749s 100 pairs aligned concordantly 0 times; of these: 749s 0 (0.00%) aligned discordantly 1 time 749s ---- 749s 100 pairs aligned 0 times concordantly or discordantly; of these: 749s 200 mates make up the pairs; of these: 749s 180 (90.00%) aligned 0 times 749s 7 (3.50%) aligned exactly 1 time 749s 13 (6.50%) aligned >1 times 749s 5 (4.72%) were unpaired; of these: 749s 5 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 10.63% overall alignment rate 749s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 749s Flattened IUPAC characters 749s Mutating sequence Sim.pm.1 749s Introducing 24 SNPs, 2/2 ref/read gaps, and 3 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutating sequence Sim.pm.2 749s Introducing 29 SNPs, 0/0 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutated reference genome to subject genome 749s SNPs introduced: 53 749s Reference gaps introduced: 2 749s Read gaps introduced: 2 749s Rearrangements introduced: 3 749s Created read sampler 749s Sampling 182 reads 749s *** Run 61 of 100 749s /usr/bin/bowtie2 --mm --rfg 6.08953529205662 -k 3 -N 1 -L21 --mp 2.32651838462523,2.10608122079489 --score-min L,3.15460502502575,5.27534903744453 --cp-ival 1 --local --trim5 1 --large-index --cp-min 6 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta 749s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 749s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 749s parsing sequence Sim.pm.1... 749s parsing sequence Sim.pm.2... 749s Parsed 166 reference bases 749s Warning: skipping read '1' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '1' because it was < 2 characters long 749s Warning: skipping read '4' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '4' because it was < 2 characters long 749s Warning: skipping read '61' because length (0) <= # seed mismatches (1) 749s Warning: skipping read '61' because it was < 2 characters long 749s Warning: skipping read '96' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '96' because it was < 2 characters long 749s Warning: skipping read '109' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '109' because it was < 2 characters long 749s Warning: skipping read '136' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '136' because it was < 2 characters long 749s Warning: skipping read '156' because length (0) <= # seed mismatches (1) 749s Warning: skipping read '156' because it was < 2 characters long 749s Warning: skipping read '157' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '157' because it was < 2 characters long 749s Read 50 alignments... 749s Warning: skipping read '161' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '161' because it was < 2 characters long 749s Read 100 alignments... 749s 182 reads; of these: 749s 182 (100.00%) were unpaired; of these: 749s 182 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 0.00% overall alignment rate 749s Read 150 alignments... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing 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line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s --- Summary --- 749s Read 1 reference strings 749s Checked 0 alignments, 0 edits 749s --------------- 749s PASSED 749s ALSO checking that bowtie2 and bowtie2-align match up 749s /usr/bin/bowtie2 --mm --rfg 6.08953529205662 -k 3 -N 1 -L21 --mp 2.32651838462523,2.10608122079489 --score-min L,3.15460502502575,5.27534903744453 --cp-ival 1 --local --trim5 1 --large-index --cp-min 6 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 749s Warning: skipping read '1' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '1' because it was < 2 characters long 749s Warning: skipping read '4' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '4' because it was < 2 characters long 749s Warning: skipping read '61' because length (0) <= # seed mismatches (1) 749s Warning: skipping read '61' because it was < 2 characters long 749s Warning: skipping read '96' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '96' because it was < 2 characters long 749s Warning: skipping read '109' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '109' because it was < 2 characters long 749s Warning: skipping read '136' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '136' because it was < 2 characters long 749s Warning: skipping read '156' because length (0) <= # seed mismatches (1) 749s Warning: skipping read '156' because it was < 2 characters long 749s Warning: skipping read '157' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '157' because it was < 2 characters long 749s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 749s Warning: skipping read '161' because length (1) <= # seed mismatches (1) 749s Warning: skipping read '161' because it was < 2 characters long 749s 182 reads; of these: 749s 182 (100.00%) were unpaired; of these: 749s 182 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 0.00% overall alignment rate 749s Flattened IUPAC characters 749s Mutating sequence Sim.pm.1 749s Introducing 5 SNPs, 2/0 ref/read gaps, and 1 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutating sequence Sim.pm.2 749s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutated reference genome to subject genome 749s SNPs introduced: 12 749s Reference gaps introduced: 3 749s Read gaps introduced: 0 749s Rearrangements introduced: 1 749s Created read sampler 749s Sampling 128 reads 749s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 749s *** Run 62 of 100 749s /usr/bin/bowtie2 --local --cp-ival 2 --large-index --np 1 --cp-min 5 --rdg 28.7958387092903 --score-min L,9.50219101863273,9.22353809000959 --nofw --gbar 4 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 749s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 749s parsing sequence Sim.pm.1... 749s parsing sequence Sim.pm.2... 749s Parsed 166 reference bases 749s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '66' because it was < 2 characters long 749s Warning: skipping mate #1 of read '85' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '85' because it was < 2 characters long 749s Warning: skipping mate #2 of read '97' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '97' because it was < 2 characters long 749s Warning: skipping mate #1 of read '99' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '99' because it was < 2 characters long 749s Warning: skipping mate #2 of read '114' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '114' because it was < 2 characters long 749s Read 50 alignments... 749s Read 100 alignments... 749s 128 reads; of these: 749s 128 (100.00%) were paired; of these: 749s 128 (100.00%) aligned concordantly 0 times 749s 0 (0.00%) aligned concordantly exactly 1 time 749s 0 (0.00%) aligned concordantly >1 times 749s ---- 749s 128 pairs aligned concordantly 0 times; of these: 749s 0 (0.00%) aligned discordantly 1 time 749s ---- 749s 128 pairs aligned 0 times concordantly or discordantly; of these: 749s 256 mates make up the pairs; of these: 749s 256 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 0.00% overall alignment rate 749s Read 150 alignments... 749s Read 200 alignments... 749s Read 250 alignments... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s 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line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s --- Summary --- 749s Read 1 reference strings 749s Checked 0 alignments, 0 edits 749s --------------- 749s PASSED 749s Flattened IUPAC characters 749s Mutating sequence Sim.pm.1 749s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutating sequence Sim.pm.2 749s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutated reference genome to subject genome 749s SNPs introduced: 5 749s Reference gaps introduced: 0 749s Read gaps introduced: 0 749s Rearrangements introduced: 1 749s Created read sampler 749s Sampling 62 reads 749s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 749s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 749s parsing sequence Sim.pm.1... 749s parsing sequence Sim.pm.2... 749s Parsed 166 reference bases 749s *** Run 63 of 100 749s /usr/bin/bowtie2 --cp-min 11 --large-index --cp-ival 1 --local --trim3 8 --score-min L,7.08986146684653,5.93545329175588 --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 749s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 749s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 749s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 749s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 749s 62 reads; of these: 749s 52 (83.87%) were paired; of these: 749s 52 (100.00%) aligned concordantly 0 times 749s 0 (0.00%) aligned concordantly exactly 1 time 749s 0 (0.00%) aligned concordantly >1 times 749s ---- 749s 52 pairs aligned concordantly 0 times; of these: 749s 0 (0.00%) aligned discordantly 1 time 749s ---- 749s 52 pairs aligned 0 times concordantly or discordantly; of these: 749s 104 mates make up the pairs; of these: 749s 104 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 10 (16.13%) were unpaired; of these: 749s 10 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 0.00% overall alignment rate 749s Read 50 alignments... 749s Read 100 alignments... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s --- Summary --- 749s Read 1 reference strings 749s Checked 0 alignments, 0 edits 749s --------------- 749s PASSED 749s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 749s /usr/bin/bowtie2 --cp-min 11 --large-index --cp-ival 1 --local --trim3 8 --score-min L,7.08986146684653,5.93545329175588 --qseq -p 4 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 749s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 749s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 749s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 749s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 749s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 750s 62 reads; of these: 750s 52 (83.87%) were paired; of these: 750s 52 (100.00%) aligned concordantly 0 times 750s 0 (0.00%) aligned concordantly exactly 1 time 750s 0 (0.00%) aligned concordantly >1 times 750s ---- 750s 52 pairs aligned concordantly 0 times; of these: 750s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 52 pairs aligned 0 times concordantly or discordantly; of these: 750s 104 mates make up the pairs; of these: 750s 104 (100.00%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 10 (16.13%) were unpaired; of these: 750s 10 (100.00%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 0.00% overall alignment rate 750s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 750s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 750s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 750s /usr/bin/bowtie2 --cp-min 11 --large-index --cp-ival 1 --local --trim3 8 --score-min L,7.08986146684653,5.93545329175588 --qseq -p 4 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 750s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 750s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 750s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 750s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 750s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 750s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 750s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 750s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 750s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 750s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 750s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 750s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 750s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 750s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 750s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 750s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 750s 62 reads; of these: 750s 52 (83.87%) were paired; of these: 750s 52 (100.00%) aligned concordantly 0 times 750s 0 (0.00%) aligned concordantly exactly 1 time 750s 0 (0.00%) aligned concordantly >1 times 750s ---- 750s 52 pairs aligned concordantly 0 times; of these: 750s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 52 pairs aligned 0 times concordantly or discordantly; of these: 750s 104 mates make up the pairs; of these: 750s 104 (100.00%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 10 (16.13%) were unpaired; of these: 750s 10 (100.00%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 0.00% overall alignment rate 750s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 750s Flattened IUPAC characters 750s Mutating sequence Sim.pm.1 750s Introducing 13 SNPs, 2/4 ref/read gaps, and 2 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutating sequence Sim.pm.2 750s Introducing 15 SNPs, 0/0 ref/read gaps, and 2 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutated reference genome to subject genome 750s SNPs introduced: 28 750s Reference gaps introduced: 2 750s Read gaps introduced: 4 750s Rearrangements introduced: 4 750s Created read sampler 750s Sampling 73 reads 750s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 750s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 750s parsing sequence Sim.pm.1... 750s parsing sequence Sim.pm.2... 750s Parsed 166 reference bases 750s *** Run 64 of 100 750s /usr/bin/bowtie2 -D 35 --score-min L,7.00694018397011,1.30303656065748 --trim3 1 --trim5 5 --norc --large-index --cp-min 5 --cp-ival 1 --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 750s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 750s Read 50 alignments... 750s 73 reads; of these: 750s 60 (82.19%) were paired; of these: 750s 60 (100.00%) aligned concordantly 0 times 750s 0 (0.00%) aligned concordantly exactly 1 time 750s 0 (0.00%) aligned concordantly >1 times 750s ---- 750s 60 pairs aligned concordantly 0 times; of these: 750s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 60 pairs aligned 0 times concordantly or discordantly; of these: 750s 120 mates make up the pairs; of these: 750s 107 (89.17%) aligned 0 times 750s 3 (2.50%) aligned exactly 1 time 750s 10 (8.33%) aligned >1 times 750s 13 (17.81%) were unpaired; of these: 750s 10 (76.92%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 3 (23.08%) aligned >1 times 750s 12.03% overall alignment rate 750s Read 100 alignments... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CGG 750s CGG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CCGGGGCGGCGGTTGC 750s CCGGGGCGGCGGTTGC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CA 750s CA 750s Processing line... 750s Processing line... 750s AGGA 750s AGGA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s TCTGAGGC 750s TCTGAGGC 750s Processing line... 750s Processing line... 750s GC 750s GC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GGC 750s GGC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GGGCCGGGGCG 750s GGGCCGGGGCG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GT 750s GT 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CCGGGGCGGCGGTTGC 750s CCGGGGCGGCGGTTGC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s AT 750s AT 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GC 750s GC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s TGCTTTAGGAGG 750s TGCTTTAGGAGG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s AT 750s AT 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GGGAGTGGGC 750s GGGAGTGGGC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CC 750s CC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s /usr/bin/bowtie2 -D 35 --score-min L,7.00694018397011,1.30303656065748 --trim3 1 --trim5 5 --norc --large-index --cp-min 5 --cp-ival 1 --qseq -p 4 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 750s --- Summary --- 750s Read 1 reference strings 750s Checked 16 alignments, 0 edits 750s --------------- 750s PASSED 750s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 750s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 750s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 750s 73 reads; of these: 750s 60 (82.19%) were paired; of these: 750s 60 (100.00%) aligned concordantly 0 times 750s 0 (0.00%) aligned concordantly exactly 1 time 750s 0 (0.00%) aligned concordantly >1 times 750s ---- 750s 60 pairs aligned concordantly 0 times; of these: 750s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 60 pairs aligned 0 times concordantly or discordantly; of these: 750s 120 mates make up the pairs; of these: 750s 107 (89.17%) aligned 0 times 750s 3 (2.50%) aligned exactly 1 time 750s 10 (8.33%) aligned >1 times 750s 13 (17.81%) were unpaired; of these: 750s 10 (76.92%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 3 (23.08%) aligned >1 times 750s 12.03% overall alignment rate 750s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 750s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 750s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 750s Flattened IUPAC characters 750s Mutating sequence Sim.pm.2 750s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutating sequence Sim.pm.1 750s Introducing 6 SNPs, 1/0 ref/read gaps, and 2 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutated reference genome to subject genome 750s SNPs introduced: 9 750s Reference gaps introduced: 1 750s Read gaps introduced: 0 750s Rearrangements introduced: 2 750s Created read sampler 750s Sampling 120 reads 750s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 750s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 750s parsing sequence Sim.pm.1... 750s parsing sequence Sim.pm.2... 750s Parsed 166 reference bases 750s *** Run 65 of 100 750s /usr/bin/bowtie2 --mp 8.95254288938183,5.22759417320858 --trim3 0 --rfg 24.667454957838 --cp-ival 1 -D 13 -k 2 -R 3 --score-min L,1.9745705126964,9.23250912817348 --ma 12.8914139572392 --large-index --cp-min 5 --np 7 -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq 750s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 750s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 750s Read 50 alignments... 750s 120 reads; of these: 750s 120 (100.00%) were unpaired; of these: 750s 97 (80.83%) aligned 0 times 750s 3 (2.50%) aligned exactly 1 time 750s 20 (16.67%) aligned >1 times 750s 19.17% overall alignment rate 750s Read 100 alignments... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s AGGAG 750s AGGAG 750s Processing line... 750s AGGAG 750s AGGAG 750s Processing line... 750s GGT 750s GGT 750s Processing line... 750s GGT 750s GGT 750s Processing line... 750s Processing line... 750s Processing line... 750s CGGTTGCTTTA 750s CGGTTGCTTTA 750s Processing line... 750s CGGTTGCTTTA 750s CGGTTGCTTTA 750s Processing line... 750s Processing line... 750s Processing line... 750s GCCGGGGCGGCGGTTGCTTTAGG 750s GCCGGGGCGGCGGTTGCTTTAGG 750s Processing line... 750s GCCGGGGCGGCGGTTGCTTTAGG 750s GCCGGGGCGGCGGTTGCTTTAGG 750s Processing line... 750s Processing line... 750s Processing line... 750s TG 750s TG 750s Processing line... 750s TG 750s TG 750s Processing line... 750s CGG 750s CGG 750s Processing line... 750s CGG 750s CGG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCG 750s CCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s ATGGGCCGGGGCGGCGGTTG 750s ATGGGCCGGGGCGGCGGTTG 750s Processing line... 750s ATGGGCCGGGGCGGCGGTTG 750s ATGGGCCGGGGCGGCGGTTG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CC 750s CC 750s Processing line... 750s CC 750s CC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GA 750s GA 750s Processing line... 750s GA 750s GA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CGG 750s CGG 750s Processing line... 750s CGG 750s CGG 750s Processing line... 750s Processing line... 750s CGGTTGCTTTAGGAGGGA 750s CGGTTGCTTTAGGAGGGA 750s Processing line... 750s CGGTTGCTTTAGGAGGGA 750s CGGTTGCTTTAGGAGGGA 750s Processing line... 750s Processing line... 750s TGGGCCGGGGCGGCGGT 750s TGGGCCGGGGCGGCGGT 750s Processing line... 750s TGGGCCGGGGCGGCGGT 750s TGGGCCGGGGCGGCGGT 750s Processing line... 750s GCGGCGGTTGCTTTAGGAG 750s GCGGCGGTTGCTTTAGGAG 750s Processing line... 750s GCGGCGGTTGCTTTAGGAG 750s GCGGCGGTTGCTTTAGGAG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GTTGCTTTAGGAGGGA 750s GTTGCTTTAGGAGGGA 750s Processing line... 750s GTTGCTTTAGGAGGGA 750s GTTGCTTTAGGAGGGA 750s Processing line... 750s Processing line... 750s Processing line... 750s TTCG 750s TTCG 750s Processing line... 750s TTCG 750s TTCG 750s Processing line... 750s Processing line... 750s Processing line... 750s TTCGG 750s TTCGG 750s Processing line... 750s TTCGG 750s TTCGG 750s Processing line... 750s Processing line... 750s Processing line... 750s GCCGGGGCGGCGGTTGCTTTAGG 750s GCCGGGGCGGCGGTTGCTTTAGG 750s Processing line... 750s GCCGGGGCGGCGGTTGCTTTAGG 750s GCCGGGGCGGCGGTTGCTTTAGG 750s Processing line... 750s Processing line... 750s Processing line... 750s TGAC 750s TGAC 750s Processing line... 750s /usr/bin/bowtie2 --mp 8.95254288938183,5.22759417320858 --trim3 0 --rfg 24.667454957838 --cp-ival 1 -D 13 -k 2 -R 3 --score-min L,1.9745705126964,9.23250912817348 --ma 12.8914139572392 --large-index --cp-min 5 --np 7 -q -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder /tmp/Sim.pm.pBDT5Pxz_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 750s TGAC 750s TGAC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CTTTAGGAGGGA 750s CTTTAGGAGGGA 750s Processing line... 750s CTTTAGGAGGGA 750s CTTTAGGAGGGA 750s Processing line... 750s CGGGTGT 750s CGGGTGT 750s Processing line... 750s GATCGGGAGTGGGCGGTTG 750s GATCGGGAGTGGGCGGTTG 750s Processing line... 750s Processing line... 750s GGCG 750s GGCG 750s Processing line... 750s GGCG 750s GGCG 750s --- Summary --- 750s Read 1 reference strings 750s Checked 43 alignments, 0 edits 750s --------------- 750s PASSED 750s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 750s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 750s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 750s 120 reads; of these: 750s 120 (100.00%) were unpaired; of these: 750s 97 (80.83%) aligned 0 times 750s 3 (2.50%) aligned exactly 1 time 750s 20 (16.67%) aligned >1 times 750s 19.17% overall alignment rate 750s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 750s Flattened IUPAC characters 750s Mutating sequence Sim.pm.2 750s Introducing 2 SNPs, 0/2 ref/read gaps, and 2 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutating sequence Sim.pm.1 750s Introducing 12 SNPs, 0/0 ref/read gaps, and 1 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutated reference genome to subject genome 750s SNPs introduced: 14 750s Reference gaps introduced: 0 750s Read gaps introduced: 2 750s Rearrangements introduced: 3 750s Created read sampler 750s Sampling 68 reads 750s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 750s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 750s parsing sequence Sim.pm.1... 750s parsing sequence Sim.pm.2... 750s *** Run 66 of 100 750s /usr/bin/bowtie2 -N 1 --trim3 5 --nofw --rfg 44.5204762333261,18.9088171358451 --norc --cp-ival 1 --score-min L,5.84899807263391,9.50548739077823 --mm --rdg 13.8355215163991,11.6840568003919 --large-index --cp-min 3 --np 1 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta 750s Parsed 166 reference bases 751s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 751s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 751s Warning: skipping read '14' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 751s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 751s Warning: skipping read '15' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 751s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 751s Warning: skipping read '28' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 751s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 751s Warning: skipping read '31' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 751s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 751s Warning: skipping read '37' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 751s Warning: skipping read '46' because length (1) <= # seed mismatches (1) 751s Warning: skipping read '46' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 751s Warning: skipping read '48' because length (1) <= # seed mismatches (1) 751s Warning: skipping read '48' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 751s Warning: skipping read '50' because length (0) <= # seed mismatches (1) 751s Warning: skipping read '50' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 751s Warning: skipping read '51' because length (1) <= # seed mismatches (1) 751s Warning: skipping read '51' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 751s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 751s Warning: skipping read '58' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 751s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 751s Warning: skipping read '62' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 751s Warning: skipping read '64' because length (0) <= # seed mismatches (1) 751s Warning: skipping read '64' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 751s 68 reads; of these: 751s 68 (100.00%) were unpaired; of these: 751s 68 (100.00%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 0.00% overall alignment rate 751s Read 50 alignments... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s --- Summary --- 751s Read 1 reference strings 751s Checked 0 alignments, 0 edits 751s --------------- 751s PASSED 751s Flattened IUPAC characters 751s Mutating sequence Sim.pm.2 751s Introducing 0 SNPs, 0/1 ref/read gaps, and 1 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutating sequence Sim.pm.1 751s Introducing 20 SNPs, 0/2 ref/read gaps, and 2 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutated reference genome to subject genome 751s SNPs introduced: 20 751s Reference gaps introduced: 0 751s Read gaps introduced: 3 751s Rearrangements introduced: 3 751s Created read sampler 751s Sampling 186 reads 751s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 751s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 751s parsing sequence Sim.pm.1... 751s parsing sequence Sim.pm.2... 751s Parsed 166 reference bases 751s *** Run 67 of 100 751s /usr/bin/bowtie2 --local --cp-ival 2 --cp-min 7 -M 3 --large-index --rdg 46.7615452933737 --mm --score-min L,6.31235587995045,4.63076405348952 -i C,3.88097173528867 --mp 9.64247340132028,8.18234048853579 --gbar 1 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 751s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 751s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '38' because it was < 2 characters long 751s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '53' because it was < 2 characters long 751s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '62' because it was < 2 characters long 751s Read 50 alignments... 751s Read 100 alignments... 751s Warning: skipping mate #2 of read '69' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '69' because it was < 2 characters long 751s Warning: skipping mate #1 of read '111' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '111' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '111' because it was < 2 characters long 751s Warning: skipping mate #2 of read '111' because it was < 2 characters long 751s Warning: skipping mate #2 of read '124' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '124' because it was < 2 characters long 751s Warning: skipping mate #2 of read '144' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '144' because it was < 2 characters long 751s Read 150 alignments... 751s Warning: skipping mate #2 of read '148' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '148' because it was < 2 characters long 751s Warning: skipping mate #2 of read '180' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '180' because it was < 2 characters long 751s Read 200 alignments... 751s 186 reads; of these: 751s 186 (100.00%) were paired; of these: 751s 186 (100.00%) aligned concordantly 0 times 751s 0 (0.00%) aligned concordantly exactly 1 time 751s 0 (0.00%) aligned concordantly >1 times 751s ---- 751s 186 pairs aligned concordantly 0 times; of these: 751s 0 (0.00%) aligned discordantly 1 time 751s ---- 751s 186 pairs aligned 0 times concordantly or discordantly; of these: 751s 372 mates make up the pairs; of these: 751s 372 (100.00%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 0.00% overall alignment rate 751s Read 250 alignments... 751s Read 300 alignments... 751s Read 350 alignments... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing 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line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s --- Summary --- 751s Read 1 reference strings 751s Checked 0 alignments, 0 edits 751s --------------- 751s PASSED 751s Flattened IUPAC characters 751s Mutating sequence Sim.pm.2 751s Introducing 24 SNPs, 0/0 ref/read gaps, and 4 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutating sequence Sim.pm.1 751s Introducing 14 SNPs, 1/0 ref/read gaps, and 0 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutated reference genome to subject genome 751s SNPs introduced: 38 751s Reference gaps introduced: 1 751s Read gaps introduced: 0 751s Rearrangements introduced: 4 751s Created read sampler 751s Sampling 66 reads 751s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 751s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 751s parsing sequence Sim.pm.1... 751s parsing sequence Sim.pm.2... 751s Parsed 166 reference bases 751s *** Run 68 of 100 751s /usr/bin/bowtie2 --rfg 34.9771987609854 --nofw --cp-ival 1 --local -M 2 --mm --rdg 3.0438446154477,3.85154055169828 --score-min L,7.97297311606944,4.25621716155599 --cp-min 8 --np 2 --large-index -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 751s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 751s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '7' because it was < 2 characters long 751s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '24' because it was < 2 characters long 751s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '30' because it was < 2 characters long 751s Read 50 alignments... 751s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '58' because it was < 2 characters long 751s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '64' because it was < 2 characters long 751s 66 reads; of these: 751s 66 (100.00%) were paired; of these: 751s 66 (100.00%) aligned concordantly 0 times 751s 0 (0.00%) aligned concordantly exactly 1 time 751s 0 (0.00%) aligned concordantly >1 times 751s ---- 751s 66 pairs aligned concordantly 0 times; of these: 751s 0 (0.00%) aligned discordantly 1 time 751s ---- 751s 66 pairs aligned 0 times concordantly or discordantly; of these: 751s 132 mates make up the pairs; of these: 751s 132 (100.00%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 0.00% overall alignment rate 751s Read 100 alignments... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s /usr/bin/bowtie2 --rfg 34.9771987609854 --nofw --cp-ival 1 --local -M 2 --mm --rdg 3.0438446154477,3.85154055169828 --score-min L,7.97297311606944,4.25621716155599 --cp-min 8 --np 2 --large-index -q -p 4 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s --- Summary --- 751s Read 1 reference strings 751s Checked 0 alignments, 0 edits 751s --------------- 751s PASSED 751s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 751s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 751s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '7' because it was < 2 characters long 751s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '24' because it was < 2 characters long 751s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '30' because it was < 2 characters long 751s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '58' because it was < 2 characters long 751s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '64' because it was < 2 characters long 751s 66 reads; of these: 751s 66 (100.00%) were paired; of these: 751s 66 (100.00%) aligned concordantly 0 times 751s 0 (0.00%) aligned concordantly exactly 1 time 751s 0 (0.00%) aligned concordantly >1 times 751s ---- 751s 66 pairs aligned concordantly 0 times; of these: 751s 0 (0.00%) aligned discordantly 1 time 751s ---- 751s 66 pairs aligned 0 times concordantly or discordantly; of these: 751s 132 mates make up the pairs; of these: 751s 132 (100.00%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 0.00% overall alignment rate 751s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 751s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 751s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 751s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 751s /usr/bin/bowtie2 --rfg 34.9771987609854 --nofw --cp-ival 1 --local -M 2 --mm --rdg 3.0438446154477,3.85154055169828 --score-min L,7.97297311606944,4.25621716155599 --cp-min 8 --np 2 --large-index -q -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 751s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 751s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '7' because it was < 2 characters long 751s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '24' because it was < 2 characters long 751s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '30' because it was < 2 characters long 751s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '58' because it was < 2 characters long 751s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '64' because it was < 2 characters long 751s 66 reads; of these: 751s 66 (100.00%) were paired; of these: 751s 66 (100.00%) aligned concordantly 0 times 751s 0 (0.00%) aligned concordantly exactly 1 time 751s 0 (0.00%) aligned concordantly >1 times 751s ---- 751s 66 pairs aligned concordantly 0 times; of these: 751s 0 (0.00%) aligned discordantly 1 time 751s ---- 751s 66 pairs aligned 0 times concordantly or discordantly; of these: 751s 132 mates make up the pairs; of these: 751s 132 (100.00%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 0.00% overall alignment rate 751s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 751s Flattened IUPAC characters 751s Mutating sequence Sim.pm.1 751s Introducing 2 SNPs, 0/2 ref/read gaps, and 0 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutating sequence Sim.pm.2 751s Introducing 9 SNPs, 1/1 ref/read gaps, and 1 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutated reference genome to subject genome 751s SNPs introduced: 11 751s Reference gaps introduced: 1 751s Read gaps introduced: 3 751s Rearrangements introduced: 1 751s Created read sampler 751s Sampling 101 reads 751s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 751s *** Run 69 of 100 751s /usr/bin/bowtie2 --cp-ival 1 --local --n-ceil 0.159489758339072,0.279442788917868 --trim5 2 --large-index --cp-min 5 --mm --rfg 2.60440519050436,5.75659535746584 --rdg 36.8257310302868 -k 3 --mp 8.21999009638054,7.13124956710088 --score-min L,6.29125372961004,6.80577309173099 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta 751s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 751s parsing sequence Sim.pm.1... 751s parsing sequence Sim.pm.2... 751s Parsed 166 reference bases 751s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '10' because it was < 2 characters long 751s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '12' because it was < 2 characters long 751s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '30' because it was < 2 characters long 751s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '71' because it was < 2 characters long 751s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '75' because it was < 2 characters long 751s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 751s Warning: skipping read '81' because it was < 2 characters long 751s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '89' because it was < 2 characters long 751s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 751s Warning: skipping read '96' because it was < 2 characters long 751s 101 reads; of these: 751s 101 (100.00%) were unpaired; of these: 751s 101 (100.00%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 0.00% overall alignment rate 751s Read 50 alignments... 751s Read 100 alignments... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s /usr/bin/bowtie2 --cp-ival 1 --local --n-ceil 0.159489758339072,0.279442788917868 --trim5 2 --large-index --cp-min 5 --mm --rfg 2.60440519050436,5.75659535746584 --rdg 36.8257310302868 -k 3 --mp 8.21999009638054,7.13124956710088 --score-min L,6.29125372961004,6.80577309173099 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s --- Summary --- 751s Read 1 reference strings 751s Checked 0 alignments, 0 edits 751s --------------- 751s PASSED 751s ALSO checking that bowtie2 and bowtie2-align match up 752s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '10' because it was < 2 characters long 752s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '12' because it was < 2 characters long 752s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '30' because it was < 2 characters long 752s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '71' because it was < 2 characters long 752s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '75' because it was < 2 characters long 752s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '81' because it was < 2 characters long 752s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '89' because it was < 2 characters long 752s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '96' because it was < 2 characters long 752s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 752s 101 reads; of these: 752s 101 (100.00%) were unpaired; of these: 752s 101 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 752s /usr/bin/bowtie2 --cp-ival 1 --local --n-ceil 0.159489758339072,0.279442788917868 --trim5 2 --large-index --cp-min 5 --mm --rfg 2.60440519050436,5.75659535746584 --rdg 36.8257310302868 -k 3 --mp 8.21999009638054,7.13124956710088 --score-min L,6.29125372961004,6.80577309173099 -f -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder /tmp/Sim.pm.pBDT5Pxz_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 752s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '10' because it was < 2 characters long 752s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '12' because it was < 2 characters long 752s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '30' because it was < 2 characters long 752s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '71' because it was < 2 characters long 752s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '75' because it was < 2 characters long 752s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '81' because it was < 2 characters long 752s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '89' because it was < 2 characters long 752s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '96' because it was < 2 characters long 752s 101 reads; of these: 752s 101 (100.00%) were unpaired; of these: 752s 101 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.2 752s Introducing 4 SNPs, 1/1 ref/read gaps, and 1 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.1 752s Introducing 8 SNPs, 1/0 ref/read gaps, and 3 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 12 752s Reference gaps introduced: 2 752s Read gaps introduced: 1 752s Rearrangements introduced: 4 752s Created read sampler 752s Sampling 75 reads 752s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 752s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s *** Run 70 of 100 752s /usr/bin/bowtie2 --large-index --np 3 --cp-min 2 --mm --rdg 36.925805540147,16.3814269837091 -R 2 --score-min L,5.6779384969849,7.88573410095992 --cp-ival 2 --local --norc --trim5 1 -i L,0.0925468475867445 --mp 6.11333187279907,5.59161604721442 --trim3 7 --nofw -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 752s Parsed 166 reference bases 752s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '3' because it was < 2 characters long 752s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '4' because it was < 2 characters long 752s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '7' because it was < 2 characters long 752s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '9' because it was < 2 characters long 752s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '10' because it was < 2 characters long 752s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '16' because it was < 2 characters long 752s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '43' because it was < 2 characters long 752s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '46' because it was < 2 characters long 752s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '47' because it was < 2 characters long 752s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '48' because it was < 2 characters long 752s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '50' because it was < 2 characters long 752s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '55' because it was < 2 characters long 752s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '70' because it was < 2 characters long 752s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '73' because it was < 2 characters long 752s 75 reads; of these: 752s 75 (100.00%) were unpaired; of these: 752s 75 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s Read 50 alignments... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s /usr/bin/bowtie2 --large-index --np 3 --cp-min 2 --mm --rdg 36.925805540147,16.3814269837091 -R 2 --score-min L,5.6779384969849,7.88573410095992 --cp-ival 2 --local --norc --trim5 1 -i L,0.0925468475867445 --mp 6.11333187279907,5.59161604721442 --trim3 7 --nofw -r -p 4 -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 0 alignments, 0 edits 752s --------------- 752s PASSED 752s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 752s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '3' because it was < 2 characters long 752s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '4' because it was < 2 characters long 752s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '7' because it was < 2 characters long 752s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '9' because it was < 2 characters long 752s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '10' because it was < 2 characters long 752s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '16' because it was < 2 characters long 752s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '43' because it was < 2 characters long 752s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '46' because it was < 2 characters long 752s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '47' because it was < 2 characters long 752s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '48' because it was < 2 characters long 752s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '50' because it was < 2 characters long 752s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '55' because it was < 2 characters long 752s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '70' because it was < 2 characters long 752s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '73' because it was < 2 characters long 752s 75 reads; of these:sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 752s 752s 75 (100.00%) were unpaired; of these: 752s 75 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 752s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.1 752s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.2 752s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 5 752s Reference gaps introduced: 0 752s Read gaps introduced: 0 752s Rearrangements introduced: 1 752s Created read sampler 752s Sampling 77 reads 752s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 752s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s *** Run 71 of 100 752s /usr/bin/bowtie2 --score-min L,8.98610131527233,5.48625021024201 --mp 7.2730166866474,2.00361749218194 -k 3 --rdg 40.1879824749094 --mm --cp-min 5 --large-index --local --cp-ival 1 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 752s Parsed 166 reference bases 752s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '30' because it was < 2 characters long 752s 77 reads; of these: 752s 77 (100.00%) were unpaired; of these: 752s 77 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s Read 50 alignments... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 0 alignments, 0 edits 752s --------------- 752s PASSED 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.1 752s Introducing 11 SNPs, 3/1 ref/read gaps, and 2 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.2 752s Introducing 3 SNPs, 2/0 ref/read gaps, and 1 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 14 752s Reference gaps introduced: 5 752s Read gaps introduced: 1 752s Rearrangements introduced: 3 752s Created read sampler 752s Sampling 76 reads 752s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 752s *** Run 72 of 100 752s /usr/bin/bowtie2 --rdg 15.5652543558025 --mm --score-min L,5.63652970181081,6.65600660618421 --trim3 4 -N 0 -L22 --mp 8.97319540508167,7.20060098825539 --cp-ival 1 --large-index --cp-min 2 --np 2 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 752s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s Parsed 166 reference bases 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 752s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read '17' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 752s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '19' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 752s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '27' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 752s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '28' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 752s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '31' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 752s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '40' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 752s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '42' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 752s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '54' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 752s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '71' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 752s Read 50 alignments... 752s Read 100 alignments... 752s 76 reads; of these: 752s 68 (89.47%) were paired; of these: 752s 67 (98.53%) aligned concordantly 0 times 752s 0 (0.00%) aligned concordantly exactly 1 time 752s 1 (1.47%) aligned concordantly >1 times 752s ---- 752s 67 pairs aligned concordantly 0 times; of these: 752s 0 (0.00%) aligned discordantly 1 time 752s ---- 752s 67 pairs aligned 0 times concordantly or discordantly; of these: 752s 134 mates make up the pairs; of these: 752s 116 (86.57%) aligned 0 times 752s 4 (2.99%) aligned exactly 1 time 752s 14 (10.45%) aligned >1 times 752s 8 (10.53%) were unpaired; of these: 752s 7 (87.50%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 1 (12.50%) aligned >1 times 752s 14.58% overall alignment rate 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s TAGGAGGGAT 752s TAGGAGGGAT 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GGGTGTCATTGTAGTGGCG 752s GGGTGTCATTGTAGTGGCG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s /usr/bin/bowtie2 --rdg 15.5652543558025 --mm --score-min L,5.63652970181081,6.65600660618421 --trim3 4 -N 0 -L22 --mp 8.97319540508167,7.20060098825539 --cp-ival 1 --large-index --cp-min 2 --np 2 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 752s Processing line... 752s TCTGAG 752s TCTGAG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s CGGGGCGGCGG 752s CGGGGCGGCGG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GGGGCGGCGGTTGCTTT 752s GGGGCGGCGGTTGCTTT 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s AGTGG 752s AGTGG 752s Processing line... 752s Processing line... 752s GGA 752s GGA 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GGGCGGCGGTTGC 752s GGGCGGCGGTTGC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s CCGGGGCGGCGGTTG 752s CCGGGGCGGCGGTTG 752s Processing line... 752s Processing line... 752s GGG 752s GGG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s ACTTTC 752s ACTTTC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s TGTC 752s TGTC 752s Processing line... 752s Processing line... 752s CCGGGGCGGCGGTTGCTTTAGG 752s CCGGGGCGGCGGTTGCTTTAGG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GGATGGGC 752s GGATGGGC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GCTTTAGGA 752s GCTTTAGGA 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s AG 752s AG 752s Processing line... 752s Processing line... 752s Processing line... 752s GTGT 752s GTGT 752s Processing line... 752s Processing line... 752s GGTGTCATTGTAGTGGCGGTCTGAGGCCGG 752s GGTGTCATTGTAGTGGCGGTCTGAGGCCGG 752s Processing line... 752s GC 752s GC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s TT 752s TT 752s Processing line... 752s Processing line... 752s CGGTTGCTT 752s CGGTTGCTT 752s Processing line... 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 21 alignments, 0 edits 752s --------------- 752s PASSED 752s ALSO checking that bowtie2 and bowtie2-align match up 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 752s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read '17' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 752s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '19' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 752s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '27' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 752s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '28' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 752s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '31' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 752s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '40' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 752s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '42' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 752s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '54' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 752s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '71' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 752s 76 reads; of these: 752s 68 (89.47%) were paired; of these: 752s 67 (98.53%) aligned concordantly 0 times 752s 0 (0.00%) aligned concordantly exactly 1 time 752s 1 (1.47%) aligned concordantly >1 times 752s ---- 752s 67 pairs aligned concordantly 0 times; of these: 752s 0 (0.00%) aligned discordantly 1 time 752s ---- 752s 67 pairs aligned 0 times concordantly or discordantly; of these: 752s 134 mates make up the pairs; of these: 752s 116 (86.57%) aligned 0 times 752s 4 (2.99%) aligned exactly 1 time 752s 14 (10.45%) aligned >1 times 752s 8 (10.53%) were unpaired; of these: 752s 7 (87.50%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 1 (12.50%) aligned >1 times 752s 14.58% overall alignment rate 752s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 752s /usr/bin/bowtie2 --rdg 15.5652543558025 --mm --score-min L,5.63652970181081,6.65600660618421 --trim3 4 -N 0 -L22 --mp 8.97319540508167,7.20060098825539 --cp-ival 1 --large-index --cp-min 2 --np 2 -r -p 2 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 752s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 752s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read '17' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 752s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '19' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 752s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '27' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 752s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '28' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 752s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '31' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 752s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '40' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 752s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '42' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 752s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '54' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 752s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '71' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 752s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 752s 76 reads; of these: 752s 68 (89.47%) were paired; of these: 752s 67 (98.53%) aligned concordantly 0 times 752s 0 (0.00%) aligned concordantly exactly 1 time 752s 1 (1.47%) aligned concordantly >1 times 752s ---- 752s 67 pairs aligned concordantly 0 times; of these: 752s 0 (0.00%) aligned discordantly 1 time 752s ---- 752s 67 pairs aligned 0 times concordantly or discordantly; of these: 752s 134 mates make up the pairs; of these: 752s 116 (86.57%) aligned 0 times 752s 4 (2.99%) aligned exactly 1 time 752s 14 (10.45%) aligned >1 times 752s 8 (10.53%) were unpaired; of these: 752s 7 (87.50%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 1 (12.50%) aligned >1 times 752s 14.58% overall alignment rate 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.1 752s Introducing 4 SNPs, 1/2 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.2 752s Introducing 4 SNPs, 1/0 ref/read gaps, and 1 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s *** Run 73 of 100 752s /usr/bin/bowtie2 --score-min L,1.03380252368432,4.43173797600797 --rdg 39.463492865859 --large-index --cp-min 2 --nofw --trim3 1 --mp 4.40867518947338,4.05186646311015 --rfg 47.2222987748195 -a --local --cp-ival 2 --qseq -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.qseq 752s Mutated reference genome to subject genome 752s SNPs introduced: 8 752s Reference gaps introduced: 2 752s Read gaps introduced: 2 752s Rearrangements introduced: 1 752s Created read sampler 752s Sampling 43 reads 752s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 752s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s Parsed 166 reference bases 752s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 752s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 752s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 752s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 752s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 752s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 752s 43 reads; of these: 752s 43 (100.00%) were unpaired; of these: 752s 43 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 0 alignments, 0 edits 752s --------------- 752s PASSED 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.1 752s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.2 752s Introducing 11 SNPs, 1/0 ref/read gaps, and 1 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 16 752s Reference gaps introduced: 2 752s Read gaps introduced: 0 752s Rearrangements introduced: 1 752s Created read sampler 752s Sampling 48 reads 752s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 752s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s Parsed 166 reference bases 752s *** Run 74 of 100 752s /usr/bin/bowtie2 --cp-ival 1 --large-index --cp-min 5 --rfg 6.15390834542094,6.68904390212555 --score-min L,4.46805072472632,4.92897681191705 --trim3 9 -D 43 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 753s Warning: skipping mate #2 of read '0' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #2 of read '0' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 753s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '8' because it was < 2 characters long 753s Warning: skipping mate #2 of read '8' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 753s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '17' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 753s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '18' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 753s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '20' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 753s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '21' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 753s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '24' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 753s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '25' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 753s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '27' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 753s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '32' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 753s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '43' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 753s 48 reads; of these: 753s 40 (83.33%) were paired; of these: 753s 40 (100.00%) aligned concordantly 0 times 753s 0 (0.00%) aligned concordantly exactly 1 time 753s 0 (0.00%) aligned concordantly >1 times 753s ---- 753s 40 pairs aligned concordantly 0 times; of these: 753s 0 (0.00%) aligned discordantly 1 time 753s ---- 753s 40 pairs aligned 0 times concordantly or discordantly; of these: 753s 80 mates make up the pairs; of these: 753s 69 (86.25%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 11 (13.75%) aligned >1 times 753s 8 (16.67%) were unpaired; of these: 753s 8 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 12.50% overall alignment rate 753s Read 50 alignments... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s GGTT 753s GGTT 753s Processing line... 753s Processing line... 753s GGAG 753s GGAG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s GCGGTTGCTTTAG 753s GCGGTTGCTTTAG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s CG 753s CG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s GGCCGG 753s GGCCGG 753s Processing line... 753s Processing line... 753s TAGGA 753s TAGGA 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s GGTTGC 753s GGTTGC 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s CTTTA 753s CTTTA 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s TCG 753s TCG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s CGGG 753s CGGG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s ATGGGCCGGGGCG 753s ATGGGCCGGGGCG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s --- Summary --- 753s Read 1 reference strings 753s Checked 11 alignments, 0 edits 753s --------------- 753s PASSED 753s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 753s /usr/bin/bowtie2 --cp-ival 1 --large-index --cp-min 5 --rfg 6.15390834542094,6.68904390212555 --score-min L,4.46805072472632,4.92897681191705 --trim3 9 -D 43 -r -p 2 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 753s Warning: skipping mate #2 of read '0' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #2 of read '0' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 753s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '8' because it was < 2 characters long 753s Warning: skipping mate #2 of read '8' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 753s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '17' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 753s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '18' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 753s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '20' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 753s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '21' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 753s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '24' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 753s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '25' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 753s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '27' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 753s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '32' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 753s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '43' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 753s 48 reads; of these: 753s 40 (83.33%) were paired; of these: 753s 40 (100.00%) aligned concordantly 0 times 753s 0 (0.00%) aligned concordantly exactly 1 time 753s 0 (0.00%) aligned concordantly >1 times 753s ---- 753s 40 pairs aligned concordantly 0 times; of these: 753s 0 (0.00%) aligned discordantly 1 time 753s ---- 753s 40 pairs aligned 0 times concordantly or discordantly; of these: 753s 80 mates make up the pairs; of these: 753s 69 (86.25%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 11 (13.75%) aligned >1 times 753s 8 (16.67%) were unpaired; of these: 753s 8 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 12.50% overall alignment rate 753s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 753s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 753s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 753s Flattened IUPAC characters 753s Mutating sequence Sim.pm.1 753s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutating sequence Sim.pm.2 753s Introducing 14 SNPs, 5/1 ref/read gaps, and 0 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutated reference genome to subject genome 753s SNPs introduced: 16 753s Reference gaps introduced: 5 753s Read gaps introduced: 2 753s Rearrangements introduced: 1 753s Created read sampler 753s Sampling 98 reads 753s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 753s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 753s parsing sequence Sim.pm.1... 753s parsing sequence Sim.pm.2... 753s Parsed 166 reference bases 753s *** Run 75 of 100 753s /usr/bin/bowtie2 -i C,0.924006122416128 -k 3 --ma 17.9641648414331 --score-min L,4.6851467696193,9.98174005255471 --cp-min 3 --large-index --cp-ival 1 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 753s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 753s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '54' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 753s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #2 of read '56' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 753s Read 50 alignments... 753s Read 100 alignments... 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 753s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #2 of read '82' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 753s Warning: skipping mate #2 of read '88' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #2 of read '88' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 753s Warning: skipping mate #1 of read '93' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '93' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 753s Read 150 alignments... 753s 98 reads; of these: 753s 98 (100.00%) were paired; of these: 753s 98 (100.00%) aligned concordantly 0 times 753s 0 (0.00%) aligned concordantly exactly 1 time 753s 0 (0.00%) aligned concordantly >1 times 753s ---- 753s 98 pairs aligned concordantly 0 times; of these: 753s 0 (0.00%) aligned discordantly 1 time 753s ---- 753s 98 pairs aligned 0 times concordantly or discordantly; of these: 753s 196 mates make up the pairs; of these: 753s 158 (80.61%) aligned 0 times 753s 7 (3.57%) aligned exactly 1 time 753s 31 (15.82%) aligned >1 times 753s 19.39% overall alignment rate 753s Read 200 alignments... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s CT 753s CT 753s Processing line... 753s CT 753s CT 753s Processing line... 753s CT 753s CT 753s Processing line... 753s Processing line... 753s AGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGC 753s AGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGC 753s Processing line... 753s Processing line... 753s GCGGCGGTTGCTTTAGGAGGGATGGG 753s GCGGCGGTTGCTTTAGGAGGGATGGG 753s Processing line... 753s GCGGCGGTTGCTTTAGGAGGGATGGG 753s GCGGCGGTTGCTTTAGGAGGGATGGG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s GGGCGG 753s GGGCGG 753s Processing line... 753s GGGCGG 753s GGGCGG 753s Processing line... 753s GGGCGG 753s GGGCGG 753s Processing line... 753s GGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 753s GGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 753s Processing line... 753s GGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 753s GGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s AT 753s AT 753s Processing line... 753s AT 753s AT 753s Processing line... 753s AT 753s AT 753s Processing line... 753s Processing line... 753s GGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTT 753s GGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTT 753s Processing line... 753s GGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTT 753s GGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTT 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s CTTTAGGAG 753s CTTTAGGAG 753s Processing line... 753s CTTTAGGAG 753s CTTTAGGAG 753s Processing line... 753s CTTTAGGAG 753s CTTTAGGAG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s TGAGG 753s TGAGG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s CGGGGCGGCGGTTGCTTTAGGAGGGA 753s CGGGGCGGCGGTTGCTTTAGGAGGGA 753s Processing line... 753s CGGGGCGGCGGTTGCTTTAGGAGGGA 753s CGGGGCGGCGGTTGCTTTAGGAGGGA 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s GGCGGTTGC 753s GGCGGTTGC 753s Processing line... 753s GGCGGTTGC 753s GGCGGTTGC 753s Processing line... 753s GGCGGTTGC 753s GGCGGTTGC 753s Processing line... 753s Processing line... 753s GTC 753s GTC 753s Processing line... 753s GAC 753s GAC 753s Processing line... 753s GAC 753s GAC 753s Processing line... 753s Processing line... 753s TTGCTTTAGGAGGGATGGGCCGGGGCGGCGGT 753s TTGCTTTAGGAGGGATGGGCCGGGGCGGCGGT 753s Processing line... 753s TTGCTTTAGGAGGGATGGGCCGGGGCGGCGGT 753s TTGCTTTAGGAGGGATGGGCCGGGGCGGCGGT 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s TGCTTTAGGAGGGATGGGCCGGGGCGGCGG 753s TGCTTTAGGAGGGATGGGCCGGGGCGGCGG 753s Processing line... 753s TGCTTTAGGAGGGATGGGCCGGGGCGGCGG 753s TGCTTTAGGAGGGATGGGCCGGGGCGGCGG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s ATGGGCCGGGGCGGCGGTTGCTTTAGGA 753s ATGGGCCGGGGCGGCGGTTGCTTTAGGA 753s Processing line... 753s ATGGGCCGGGGCGGCGGTTGCTTTAGGA 753s ATGGGCCGGGGCGGCGGTTGCTTTAGGA 753s Processing line... 753s Processing line... 753s GGCGGTT 753s GGCGGTT 753s Processing line... 753s GGCGGTT 753s GGCGGTT 753s Processing line... 753s GGCGGTT 753s GGCGGTT 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s ATTGT 753s ATTGT 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s GGATGGGCCGGGGCGGCGGTTG 753s GGATGGGCCGGGGCGGCGGTTG 753s Processing line... 753s GGATGGGCCGGGGCGGCGGTTG 753s GGATGGGCCGGGGCGGCGGTTG 753s Processing line... 753s Processing line... 753s TAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATG 753s TAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s TGCTTTAGGAGGGATGGGCCGGGG 753s TGCTTTAGGAGGGATGGGCCGGGG 753s Processing line... 753s TGCTTTAGGAGGGATGGGCCGGGG 753s TGCTTTAGGAGGGATGGGCCGGGG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s GGGAGTGGGCGGTTGACTT 753s GGGAGTGGGCGGTTGACTT 753s Processing line... 753s Processing line... 753s CGGGGCGGCGGTTGCTT 753s CGGGGCGGCGGTTGCTT 753s Processing line... 753s CGGGGCGGCGGTTGCTT 753s CGGGGCGGCGGTTGCTT 753s Processing line... 753s CGGGGCGGCGGTTGCTT 753s CGGGGCGGCGGTTGCTT 753s Processing line... 753s Processing line... 753s GGGC 753s GGGC 753s Processing line... 753s GGGC 753s GGGC 753s Processing line... 753s GGGC 753s GGGC 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s CTTTAGGAGGG 753s CTTTAGGAGGG 753s Processing line... 753s CTTTAGGAGGG 753s CTTTAGGAGGG 753s Processing line... 753s CTTTAGGAGGG 753s CTTTAGGAGGG 753s Processing line... 753s GCGGTTGCTTTAGGAGGGATGGGCCG 753s GCGGTTGCTTTAGGAGGGATGGGCCG 753s Processing line... 753s GCGGTTGCTTTAGGAGGGATGGGCCG 753s GCGGTTGCTTTAGGAGGGATGGGCCG 753s Processing line... 753s Processing line... 753s Processing line... 753s CTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGG 753s CTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s AGGAGGGATGGGCCGGGGCGGCGGTTGC 753s AGGAGGGATGGGCCGGGGCGGCGGTTGC 753s Processing line... 753s AGGAGGGATGGGCCGGGGCGGCGGTTGC 753s AGGAGGGATGGGCCGGGGCGGCGGTTGC 753s Processing line... 753s Processing line... 753s TG 753s TG 753s Processing line... 753s TG 753s TG 753s Processing line... 753s TG 753s TG 753s Processing line... 753s Processing line... 753s TTGACTTTCGGGTGT 753s TTGACTTTCGGGTGT 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s AGGAGGGATGGGCCGGGGCGGC 753s AGGAGGGATGGGCCGGGGCGGC 753s Processing line... 753s AGGAGGGATGGGCCGGGGCGGC 753s AGGAGGGATGGGCCGGGGCGGC 753s Processing line... 753s Processing line... 753s TAGGAGGGATGGGCCGGGGCGGCGGTTGCT 753s TAGGAGGGATGGGCCGGGGCGGCGGTTGCT 753s Processing line... 753s TAGGAGGGATGGGCCGGGGCGGCGGTTGCT 753s TAGGAGGGATGGGCCGGGGCGGCGGTTGCT 753s Processing line... 753s Processing line... 753s GCGGC 753s GCGGC 753s Processing line... 753s GCGGC 753s GCGGC 753s Processing line... 753s GCGGC 753s GCGGC 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s GCC 753s GCC 753s Processing line... 753s GCC 753s GCC 753s Processing line... 753s GCC 753s GCC 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s GAC 753s GAC 753s Processing line... 753s GTC 753s GTC 753s Processing line... 753s GTC 753s GTC 753s Processing line... 753s Processing line... 753s GGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 753s GGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 753s Processing line... 753s GGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 753s GGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s TTAGGAGGGATGGGCCGGGGCGG 753s TTAGGAGGGATGGGCCGGGGCGG 753s Processing line... 753s TTAGGAGGGATGGGCCGGGGCGG 753s TTAGGAGGGATGGGCCGGGGCGG 753s Processing line... 753s Processing line... 753s GGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTA 753s GGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTA 753s Processing line... 753s GGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTA 753s GGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTA 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s GGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTT 753s GGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTT 753s Processing line... 753s GGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTT 753s GGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTT 753s Processing line... 753s --- Summary --- 753s Read 1 reference strings 753s Checked 83 alignments, 0 edits 753s --------------- 753s PASSED 753s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 753s /usr/bin/bowtie2 -i C,0.924006122416128 -k 3 --ma 17.9641648414331 --score-min L,4.6851467696193,9.98174005255471 --cp-min 3 --large-index --cp-ival 1 -q -p 2 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 753s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 753s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #2 of read '82' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 753s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '54' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 753s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #2 of read '56' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 753s Warning: skipping mate #2 of read '88' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #2 of read '88' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 753s Warning: skipping mate #1 of read '93' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '93' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 753s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 753s 98 reads; of these: 753s 98 (100.00%) were paired; of these: 753s 98 (100.00%) aligned concordantly 0 times 753s 0 (0.00%) aligned concordantly exactly 1 time 753s 0 (0.00%) aligned concordantly >1 times 753s ---- 753s 98 pairs aligned concordantly 0 times; of these: 753s 0 (0.00%) aligned discordantly 1 time 753s ---- 753s 98 pairs aligned 0 times concordantly or discordantly; of these: 753s 196 mates make up the pairs; of these: 753s 158 (80.61%) aligned 0 times 753s 7 (3.57%) aligned exactly 1 time 753s 31 (15.82%) aligned >1 times 753s 19.39% overall alignment rate 753s Flattened IUPAC characters 753s Mutating sequence Sim.pm.1 753s Introducing 11 SNPs, 0/1 ref/read gaps, and 2 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutating sequence Sim.pm.2 753s Introducing 14 SNPs, 2/2 ref/read gaps, and 2 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutated reference genome to subject genome 753s SNPs introduced: 25 753s Reference gaps introduced: 2 753s Read gaps introduced: 3 753s Rearrangements introduced: 4 753s Created read sampler 753s Sampling 43 reads 753s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 753s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 753s parsing sequence Sim.pm.1... 753s parsing sequence Sim.pm.2... 753s Parsed 166 reference bases 753s *** Run 76 of 100 753s /usr/bin/bowtie2 --mm --gbar 2 --score-min L,2.25557864723922,9.82916490429967 --large-index --np 1 --cp-min 5 --rfg 27.6675459424692,2.46133117806779 --mp 5.94397770438255,4.58047414959423 --trim3 9 --cp-ival 1 --local --n-ceil 0.114217797624186,1.23114775663594 -M 3 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 753s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 753s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '1' because it was < 2 characters long 753s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '18' because it was < 2 characters long 753s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '19' because it was < 2 characters long 753s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '29' because it was < 2 characters long 753s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '37' because it was < 2 characters long 753s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '38' because it was < 2 characters long 753s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '39' because it was < 2 characters long 753s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '42' because it was < 2 characters long 753s 43 reads; of these: 753s 36 (83.72%) were paired; of these: 753s 36 (100.00%) aligned concordantly 0 times 753s 0 (0.00%) aligned concordantly exactly 1 time 753s 0 (0.00%) aligned concordantly >1 times 753s ---- 753s 36 pairs aligned concordantly 0 times; of these: 753s 0 (0.00%) aligned discordantly 1 time 753s ---- 753s 36 pairs aligned 0 times concordantly or discordantly; of these: 753s 72 mates make up the pairs; of these: 753s 72 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 7 (16.28%) were unpaired; of these: 753s 7 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s Read 50 alignments... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s /usr/bin/bowtie2 --mm --gbar 2 --score-min L,2.25557864723922,9.82916490429967 --large-index --np 1 --cp-min 5 --rfg 27.6675459424692,2.46133117806779 --mp 5.94397770438255,4.58047414959423 --trim3 9 --cp-ival 1 --local --n-ceil 0.114217797624186,1.23114775663594 -M 3 -r -p 3 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s --- Summary --- 753s Read 1 reference strings 753s Checked 0 alignments, 0 edits 753s --------------- 753s PASSED 753s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 753s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 753s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '1' because it was < 2 characters long 753s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '18' because it was < 2 characters long 753s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '19' because it was < 2 characters long 753s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '29' because it was < 2 characters long 753s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '37' because it was < 2 characters long 753s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '38' because it was < 2 characters long 753s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '39' because it was < 2 characters long 753s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '42' because it was < 2 characters long 753s 43 reads; of these: 753s 36 (83.72%) were paired; of these: 753s 36 (100.00%) aligned concordantly 0 times 753s 0 (0.00%) aligned concordantly exactly 1 time 753s 0 (0.00%) aligned concordantly >1 times 753s ---- 753s 36 pairs aligned concordantly 0 times; of these: 753s 0 (0.00%) aligned discordantly 1 time 753s ---- 753s 36 pairs aligned 0 times concordantly or discordantly; of these: 753s 72 mates make up the pairs; of these: 753s 72 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 7 (16.28%) were unpaired; of these: 753s 7 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 754s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 754s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 754s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 754s /usr/bin/bowtie2 --mm --gbar 2 --score-min L,2.25557864723922,9.82916490429967 --large-index --np 1 --cp-min 5 --rfg 27.6675459424692,2.46133117806779 --mp 5.94397770438255,4.58047414959423 --trim3 9 --cp-ival 1 --local --n-ceil 0.114217797624186,1.23114775663594 -M 3 -r -p 4 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 754s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 754s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '1' because it was < 2 characters long 754s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '18' because it was < 2 characters long 754s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '19' because it was < 2 characters long 754s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '29' because it was < 2 characters long 754s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '37' because it was < 2 characters long 754s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '38' because it was < 2 characters long 754s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '39' because it was < 2 characters long 754s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '42' because it was < 2 characters long 754s 43 reads; of these: 754s 36 (83.72%) were paired; of these: 754s 36 (100.00%) aligned concordantly 0 times 754s 0 (0.00%) aligned concordantly exactly 1 time 754s 0 (0.00%) aligned concordantly >1 times 754s ---- 754s 36 pairs aligned concordantly 0 times; of these: 754s 0 (0.00%) aligned discordantly 1 time 754s ---- 754s 36 pairs aligned 0 times concordantly or discordantly; of these: 754s 72 mates make up the pairs; of these: 754s 72 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 7 (16.28%) were unpaired; of these: 754s 7 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 0.00% overall alignment rate 754s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.2 754s Introducing 17 SNPs, 0/1 ref/read gaps, and 1 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.1 754s Introducing 14 SNPs, 4/1 ref/read gaps, and 1 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 31 754s Reference gaps introduced: 4 754s Read gaps introduced: 2 754s Rearrangements introduced: 2 754s Created read sampler 754s Sampling 65 reads 754s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 754s *** Run 77 of 100 754s /usr/bin/bowtie2 -R 1 --score-min L,6.15622930241725,4.60205321767112 --mm --rdg 1.23360967024081,19.1997522199428 --large-index --cp-min 2 --np 3 --mp 9.31666469244124,2.65402318006008 --rfg 36.7638165522015 --trim5 0 -M 4 --cp-ival 1 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 754s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 166 reference bases 754s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 754s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '13' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 754s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #2 of read '28' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 754s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '29' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 754s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '39' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 754s Read 50 alignments... 754s Read 100 alignments... 754s 65 reads; of these: 754s 65 (100.00%) were paired; of these: 754s 65 (100.00%) aligned concordantly 0 times 754s 0 (0.00%) aligned concordantly exactly 1 time 754s 0 (0.00%) aligned concordantly >1 times 754s ---- 754s 65 pairs aligned concordantly 0 times; of these: 754s 0 (0.00%) aligned discordantly 1 time 754s ---- 754s 65 pairs aligned 0 times concordantly or discordantly; of these: 754s 130 mates make up the pairs; of these: 754s 116 (89.23%) aligned 0 times 754s 4 (3.08%) aligned exactly 1 time 754s 10 (7.69%) aligned >1 times 754s 10.77% overall alignment rate 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GC 754s GC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TTCG 754s TTCG 754s Processing line... 754s Processing line... 754s GG 754s GG 754s Processing line... 754s Processing line... 754s AGTGGGCGGT 754s AGTGGGCGGT 754s Processing line... 754s GGCG 754s GGCG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AGTGGGCGGTTGAC 754s AGTGGGCGGTTGAC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGCGGTTGC 754s GGCGGTTGC 754s Processing line... 754s CGGTCTG 754s CGGTCTG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGGGCGGCGGTT 754s GGGGCGGCGGTT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GC 754s GC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGGC 754s GGGC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGAGTGGG 754s GGAGTGGG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GG 754s GG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGT 754s GGT 754s Processing line... 754s Processing line... 754s Processing line... 754s --- Summary --- 754s Read 1 reference strings 754s Checked 14 alignments, 0 edits 754s --------------- 754s PASSED 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.2 754s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.1 754s Introducing 10 SNPs, 1/1 ref/read gaps, and 1 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 15 754s Reference gaps introduced: 1 754s Read gaps introduced: 1 754s Rearrangements introduced: 1 754s Created read sampler 754s Sampling 62 reads 754s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 754s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 754s parsing sequence Sim.pm.1... 754s *** Run 78 of 100 754s /usr/bin/bowtie2 -N 0 --score-min L,3.99506796923502,8.75291459308832 --cp-ival 2 --local --cp-min 2 --np 1 --large-index -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq 754s parsing sequence Sim.pm.2... 754s Parsed 166 reference bases 754s 62 reads; of these: 754s 62 (100.00%) were unpaired; of these: 754s 62 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 0.00% overall alignment rate 754s Read 50 alignments... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s --- Summary --- 754s Read 1 reference strings 754s Checked 0 alignments, 0 edits 754s --------------- 754s PASSED 754s ALSO checking that bowtie2 and bowtie2-align match up 754s /usr/bin/bowtie2 -N 0 --score-min L,3.99506796923502,8.75291459308832 --cp-ival 2 --local --cp-min 2 --np 1 --large-index -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 754s 62 reads; of these: 754s 62 (100.00%) were unpaired; of these: 754s 62 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 0.00% overall alignment rate 754s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.2 754s Introducing 4 SNPs, 1/1 ref/read gaps, and 4 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.1 754s Introducing 13 SNPs, 0/0 ref/read gaps, and 1 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 17 754s Reference gaps introduced: 1 754s Read gaps introduced: 1 754s Rearrangements introduced: 5 754s Created read sampler 754s Sampling 127 reads 754s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 754s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 166 reference bases 754s *** Run 79 of 100 754s /usr/bin/bowtie2 --large-index -M 5 --cp-min 2 --cp-ival 5 -R 1 --score-min L,9.12728922433201,1.06790101238135 --ma 22.6510754299077 --mm --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 754s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 754s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 754s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 754s Warning: skipping mate #2 of read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #2 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 754s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 754s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 754s Read 50 alignments... 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 754s Warning: skipping mate #2 of read 'R_1_1_1_120_120_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #2 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 754s 127 reads; of these: 754s 127 (100.00%) were paired; of these: 754s 126 (99.21%) aligned concordantly 0 times 754s 0 (0.00%) aligned concordantly exactly 1 time 754s 1 (0.79%) aligned concordantly >1 times 754s ---- 754s 126 pairs aligned concordantly 0 times; of these: 754s 0 (0.00%) aligned discordantly 1 time 754s ---- 754s 126 pairs aligned 0 times concordantly or discordantly; of these: 754s 252 mates make up the pairs; of these: 754s 215 (85.32%) aligned 0 times 754s 11 (4.37%) aligned exactly 1 time 754s 26 (10.32%) aligned >1 times 754s 15.35% overall alignment rate 754s Read 100 alignments... 754s Read 150 alignments... 754s Read 200 alignments... 754s Read 250 alignments... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CGGGT 754s CGGGT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TTAGGAGGG 754s TTAGGAGGG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGGAGTGG 754s GGGAGTGG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GATGGGCCGGGGCGGCGG 754s GATGGGCCGGGGCGGCGG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GAGGGATGGGCCGG 754s GAGGGATGGGCCGG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGAG 754s GGAG 754s Processing line... 754s Processing line... 754s CTG 754s CTG 754s Processing line... 754s GGCCGGGGCGGCGGTTGCT 754s GGCCGGGGCGGCGGTTGCT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 754s GGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 754s Processing line... 754s Processing line... 754s TTTAGGAGGGATGGGCCGGG 754s TTTAGGAGGGATGGGCCGGG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGCGGTT 754s GGCGGTT 754s Processing line... 754s Processing line... 754s GGAGTGGGCGGTTGACTTTC 754s GGAGTGGGCGGTTGACTTTC 754s Processing line... 754s Processing line... 754s CGGGAGTGGGCGGTTGACTTTC 754s CGGGAGTGGGCGGTTGACTTTC 754s Processing line... 754s Processing line... 754s AGT 754s AGT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGAGT 754s GGAGT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGCGGT 754s GGCGGT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGCGGTTGACTTTCGGGTGTCA 754s GGCGGTTGACTTTCGGGTGTCA 754s Processing line... 754s GTC 754s GTC 754s Processing line... 754s TTTCGGC 754s TTTCGGC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GTGG 754s GTGG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TGGGCCGGGGCGGCGGTTGCTTT 754s TGGGCCGGGGCGGCGGTTGCTTT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AGTGG 754s AGTGG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGGCC 754s GGGCC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TCATTGTA 754s TCATTGTA 754s Processing line... 754s Processing line... 754s GGAGGGATGGGCCGGGGCG 754s GGAGGGATGGGCCGGGGCG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GAGGGATGGGCCGGG 754s GAGGGATGGGCCGGG 754s Processing line... 754s Processing line... 754s CTTT 754s CTTT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GCT 754s GCT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TGGGCGGTTGAC 754s TGGGCGGTTGAC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CGGCGG 754s CGGCGG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AGTGGCGGTCTGAGGCC 754s AGTGGCGGTCTGAGGCC 754s Processing line... 754s Processing line... 754s GGGCGGCGGTTGCTTTAGG 754s GGGCGGCGGTTGCTTTAGG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s *** Run 80 of 100 754s /usr/bin/bowtie2 --rdg 36.5811889941809,18.486727927519 --rfg 43.6201201824985,3.93963542714203 --score-min L,7.72458664169063,2.85631906324398 --mp 4.24701833259154,2.18058415984253 -i L,0.270766309469536 --local --cp-ival 1 --cp-min 6 --large-index --trim5 4 --qseq -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.qseq 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CATTGTAGTGGCG 754s CATTGTAGTGGCG 754s Processing line... 754s Processing line... 754s GGCGGTTGACTTT 754s GGCGGTTGACTTT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AGGCCGG 754s AGGCCGG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGC 754s GGC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TGCTTTAGGAGGGATGGGCC 754s TGCTTTAGGAGGGATGGGCC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GGCCGGGGCGGCGGTTG 754s GGCCGGGGCGGCGGTTG 754s Processing line... 754s Processing line... 754s GC 754s GC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s --- Summary --- 754s Read 1 reference strings 754s Checked 39 alignments, 0 edits 754s --------------- 754s PASSED 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.1 754s Introducing 11 SNPs, 0/0 ref/read gaps, and 2 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.2 754s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 19 754s Reference gaps introduced: 0 754s Read gaps introduced: 1 754s Rearrangements introduced: 2 754s Created read sampler 754s Sampling 117 reads 754s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 754s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 166 reference bases 754s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 754s 117 reads; of these: 754s 117 (100.00%) were unpaired; of these: 754s 117 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 0.00% overall alignment rate 754s Read 50 alignments... 754s Read 100 alignments... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s --- Summary --- 754s Read 1 reference strings 754s Checked 0 alignments, 0 edits 754s --------------- 754s PASSED 754s ALSO checking that bowtie2 and bowtie2-align match up 754s /usr/bin/bowtie2 --rdg 36.5811889941809,18.486727927519 --rfg 43.6201201824985,3.93963542714203 --score-min L,7.72458664169063,2.85631906324398 --mp 4.24701833259154,2.18058415984253 -i L,0.270766309469536 --local --cp-ival 1 --cp-min 6 --large-index --trim5 4 --qseq -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 754s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 754s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 754s 117 reads; of these: 754s 117 (100.00%) were unpaired; of these: 754s 117 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 0.00% overall alignment rate 754s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.2 754s Introducing 13 SNPs, 0/0 ref/read gaps, and 3 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.1 754s Introducing 1 SNPs, 1/0 ref/read gaps, and 1 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 14 754s Reference gaps introduced: 1 754s Read gaps introduced: 0 754s Rearrangements introduced: 4 754s Created read sampler 754s Sampling 24 reads 754s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 754s *** Run 81 of 100 754s /usr/bin/bowtie2 -D 19 --gbar 3 --ma 18.8704403210373 --score-min L,9.58873699281488,9.37342930666241 --cp-min 2 --np 6 --large-index --mp 3.65924259230291,1.22817199695605 --rfg 35.6236563851176 --n-ceil 0.779379454323675,0.47524249013309 -a --cp-ival 4 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 754s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 166 reference bases 754s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 754s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #2 of read '9' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 754s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #2 of read '18' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 754s 24 reads; of these: 754s 24 (100.00%) were paired; of these: 754s 23 (95.83%) aligned concordantly 0 times 754s 0 (0.00%) aligned concordantly exactly 1 time 754s 1 (4.17%) aligned concordantly >1 times 754s ---- 754s 23 pairs aligned concordantly 0 times; of these: 754s 0 (0.00%) aligned discordantly 1 time 754s ---- 754s 23 pairs aligned 0 times concordantly or discordantly; of these: 754s 46 mates make up the pairs; of these: 754s 36 (78.26%) aligned 0 times 754s 3 (6.52%) aligned exactly 1 time 754s 7 (15.22%) aligned >1 times 754s 25.00% overall alignment rate 754s Read 50 alignments... 754s Read 100 alignments... 754s Read 150 alignments... 754s Read 200 alignments... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CCG 754s CCG 754s Processing line... 754s CCG 754s CCG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CCG 754s CCG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s Processing line... 754s TGGGCGGTTGACTTTCGGGTGTCAT 754s TGGGCGGTTGACTTTCGGGTGTCAT 754s Processing line... 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CCG 754s CCG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CCG 754s CCG 754s Processing line... 754s CCG 754s CCG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s CGG 754s CGG 754s Processing line... 754s Processing line... 754s GCCGGGGC 754s GCCGGGGC 754s Processing line... 754s GCCGGGGC 754s GCCGGGGC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CGGCGGTTGCTTTA 754s CGGCGGTTGCTTTA 754s Processing line... 754s CGGCGGTTGCTTTA 754s CGGCGGTTGCTTTA 754s Processing line... 754s CGGCGGTTGCTTTA 754s CGGCGGTTGCTTTA 754s Processing line... 754s Processing line... 754s TTA 754s TTA 754s Processing line... 754s TTA 754s TTA 754s Processing line... 754s TTA 754s TTA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GCCGGGGC 754s GCCGGGGC 754s Processing line... 754s GCCGGGGC 754s GCCGGGGC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CGGC 754s CGGC 754s Processing line... 754s GCCG 754s GCCG 754s Processing line... 754s CGGC 754s CGGC 754s Processing line... 754s CGGC 754s CGGC 754s Processing line... 754s GCCG 754s GCCG 754s Processing line... 754s CGGC 754s CGGC 754s Processing line... 754s GCCG 754s GCCG 754s Processing line... 754s Processing line... 754s GGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTG 754s GGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTG 754s Processing line... 754s Processing line... 754s AGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGC 754s AGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGC 754s Processing line... 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s CT 754s CT 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s Processing line... 754s AG 754s AG 754s Processing line... 754s GC 754s GC 754s --- Summary --- 754s Read 1 reference strings 754s Checked 194 alignments, 0 edits 754s --------------- 754s PASSED 754s *** Run 82 of 100 754s /usr/bin/bowtie2 -R 4 --gbar 1 --ma 19.1882883771344 --score-min L,2.94788197128566,4.71284993299853 --np 6 --cp-min 4 --large-index --mp 6.66734283730581,4.11406150306353 -N 1 -L20 -i S,0.54821262629613 --norc --n-ceil 0.538143706853602,0.040178509156766 -M 2 --cp-ival 1 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.2 754s Introducing 6 SNPs, 1/4 ref/read gaps, and 1 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.1 754s Introducing 6 SNPs, 1/0 ref/read gaps, and 3 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 12 754s Reference gaps introduced: 2 754s Read gaps introduced: 4 754s Rearrangements introduced: 4 754s Created read sampler 754s Sampling 100 reads 754s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 754s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 166 reference bases 755s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 755s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 755s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #2 of read '12' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 755s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '49' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 755s Read 50 alignments... 755s Read 100 alignments... 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 755s Warning: skipping mate #1 of read '69' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '69' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 755s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #2 of read '89' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 755s 100 reads; of these: 755s 100 (100.00%) were paired; of these: 755s 100 (100.00%) aligned concordantly 0 times 755s 0 (0.00%) aligned concordantly exactly 1 time 755s 0 (0.00%) aligned concordantly >1 times 755s ---- 755s 100 pairs aligned concordantly 0 times; of these: 755s 0 (0.00%) aligned discordantly 1 time 755s ---- 755s 100 pairs aligned 0 times concordantly or discordantly; of these: 755s 200 mates make up the pairs; of these: 755s 178 (89.00%) aligned 0 times 755s 5 (2.50%) aligned exactly 1 time 755s 17 (8.50%) aligned >1 times 755s 11.00% overall alignment rate 755s Read 150 alignments... 755s Read 200 alignments... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s /usr/bin/bowtie2 -R 4 --gbar 1 --ma 19.1882883771344 --score-min L,2.94788197128566,4.71284993299853 --np 6 --cp-min 4 --large-index --mp 6.66734283730581,4.11406150306353 -N 1 -L20 -i S,0.54821262629613 --norc --n-ceil 0.538143706853602,0.040178509156766 -M 2 --cp-ival 1 -q -p 2 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GTTGC 755s GTTGC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GGCCGG 755s GGCCGG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GCCGGGGCG 755s GCCGGGGCG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CCG 755s CCG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TTAGGAGGGATG 755s TTAGGAGGGATG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CCGGGGCGGCGGTTGCTTTAGGAGGGA 755s CCGGGGCGGCGGTTGCTTTAGGAGGGA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GGGT 755s GGGT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s AG 755s AG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CG 755s CG 755s Processing line... 755s Processing line... 755s CGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCG 755s CGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CC 755s CC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GC 755s GC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GCTTTAGGAGGG 755s GCTTTAGGAGGG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GTGTCATTGTAGTGG 755s GTGTCATTGTAGTGG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TGGG 755s TGGG 755s Processing line... 755s Processing line... 755s CC 755s CC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GGGATGG 755s GGGATGG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GAT 755s GAT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TTAGGA 755s TTAGGA 755s Processing line... 755s Processing line... 755s GGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 755s GGATGGGCCGGGGCGGCGGTTGCTTTAGGAG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CGGGGCGGCGGTTGCTTTAG 755s CGGGGCGGCGGTTGCTTTAG 755s Processing line... 755s Processing line... 755s GTA 755s GTA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 22 alignments, 0 edits 755s --------------- 755s PASSED 755s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 755s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 755s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 755s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #2 of read '12' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 755s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '49' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 755s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #2 of read '89' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 755s Warning: skipping mate #1 of read '69' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '69' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 755s 100 reads; of these: 755s 100 (100.00%) were paired; of these: 755s 100 (100.00%) aligned concordantly 0 times 755s 0 (0.00%) aligned concordantly exactly 1 time 755s 0 (0.00%) aligned concordantly >1 times 755s ---- 755s 100 pairs aligned concordantly 0 times; of these: 755s 0 (0.00%) aligned discordantly 1 time 755s ---- 755s 100 pairs aligned 0 times concordantly or discordantly; of these: 755s 200 mates make up the pairs; of these: 755s 178 (89.00%) aligned 0 times 755s 5 (2.50%) aligned exactly 1 time 755s 17 (8.50%) aligned >1 times 755s 11.00% overall alignment rate 755s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 755s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 755s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 755s /usr/bin/bowtie2 -R 4 --gbar 1 --ma 19.1882883771344 --score-min L,2.94788197128566,4.71284993299853 --np 6 --cp-min 4 --large-index --mp 6.66734283730581,4.11406150306353 -N 1 -L20 -i S,0.54821262629613 --norc --n-ceil 0.538143706853602,0.040178509156766 -M 2 --cp-ival 1 -q -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 755s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 755s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 755s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 755s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #2 of read '12' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 755s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '49' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 755s Warning: skipping mate #1 of read '69' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '69' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 755s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #2 of read '89' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 755s 100 reads; of these: 755s 100 (100.00%) were paired; of these: 755s 100 (100.00%) aligned concordantly 0 times 755s 0 (0.00%) aligned concordantly exactly 1 time 755s 0 (0.00%) aligned concordantly >1 times 755s ---- 755s 100 pairs aligned concordantly 0 times; of these: 755s 0 (0.00%) aligned discordantly 1 time 755s ---- 755s 100 pairs aligned 0 times concordantly or discordantly; of these: 755s 200 mates make up the pairs; of these: 755s 178 (89.00%) aligned 0 times 755s 5 (2.50%) aligned exactly 1 time 755s 17 (8.50%) aligned >1 times 755s 11.00% overall alignment rate 755s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.1 755s Introducing 10 SNPs, 0/0 ref/read gaps, and 4 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.2 755s Introducing 20 SNPs, 1/0 ref/read gaps, and 1 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 30 755s Reference gaps introduced: 1 755s Read gaps introduced: 0 755s Rearrangements introduced: 5 755s Created read sampler 755s Sampling 75 reads 755s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 755s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 755s parsing sequence Sim.pm.1... 755s parsing sequence Sim.pm.2... 755s Parsed 166 reference bases 755s *** Run 83 of 100 755s /usr/bin/bowtie2 --rfg 21.1254774391025,9.48576822471353 -i L,0.00560664174918297,2.34861732629709 --mp 4.74641504764803,1.21315541449851 --cp-ival 1 --local --norc --rdg 16.969117839064,14.704529949876 -k 7 --score-min L,1.4308053523388,4.8791375526817 --large-index --cp-min 2 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 755s Warning: skipping mate #1 of read '4' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '4' because it was < 2 characters long 755s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #2 of read '42' because it was < 2 characters long 755s Read 50 alignments... 755s 75 reads; of these: 755s 75 (100.00%) were paired; of these: 755s 75 (100.00%) aligned concordantly 0 times 755s 0 (0.00%) aligned concordantly exactly 1 time 755s 0 (0.00%) aligned concordantly >1 times 755s ---- 755s 75 pairs aligned concordantly 0 times; of these: 755s 0 (0.00%) aligned discordantly 1 time 755s ---- 755s 75 pairs aligned 0 times concordantly or discordantly; of these: 755s 150 mates make up the pairs; of these: 755s 150 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 0.00% overall alignment rate 755s Read 100 alignments... 755s Read 150 alignments... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 0 alignments, 0 edits 755s --------------- 755s PASSED 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.1 755s Introducing 6 SNPs, 0/1 ref/read gaps, and 1 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.2 755s Introducing 18 SNPs, 2/6 ref/read gaps, and 1 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 24 755s Reference gaps introduced: 2 755s Read gaps introduced: 7 755s Rearrangements introduced: 2 755s Created read sampler 755s Sampling 44 reads 755s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 755s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 755s parsing sequence Sim.pm.1... 755s parsing sequence Sim.pm.2... 755s Parsed 166 reference bases 755s *** Run 84 of 100 755s /usr/bin/bowtie2 --cp-ival 1 --local --cp-min 2 --large-index --trim3 8 --nofw --score-min L,1.02431218049793,4.87472422483915 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta 755s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '5' because it was < 2 characters long 755s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '10' because it was < 2 characters long 755s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '14' because it was < 2 characters long 755s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '15' because it was < 2 characters long 755s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '17' because it was < 2 characters long 755s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '28' because it was < 2 characters long 755s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '37' because it was < 2 characters long 755s /usr/bin/bowtie2 --cp-ival 1 --local --cp-min 2 --large-index --trim3 8 --nofw --score-min L,1.02431218049793,4.87472422483915 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 755s 44 reads; of these: 755s 44 (100.00%) were unpaired; of these: 755s 44 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 0.00% overall alignment rate 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 0 alignments, 0 edits 755s --------------- 755s PASSED 755s ALSO checking that bowtie2 and bowtie2-align match up 755s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '5' because it was < 2 characters long 755s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '10' because it was < 2 characters long 755s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '14' because it was < 2 characters long 755s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '15' because it was < 2 characters long 755s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '17' because it was < 2 characters long 755s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '28' because it was < 2 characters long 755s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '37' because it was < 2 characters long 755s 44 reads; of these: 755s 44 (100.00%) were unpaired; of these: 755s 44 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 0.00% overall alignment rate 755s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 755s /usr/bin/bowtie2 --cp-ival 1 --local --cp-min 2 --large-index --trim3 8 --nofw --score-min L,1.02431218049793,4.87472422483915 -f -p 2 -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 755s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 755s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '5' because it was < 2 characters long 755s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '10' because it was < 2 characters long 755s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '14' because it was < 2 characters long 755s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '15' because it was < 2 characters long 755s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '17' because it was < 2 characters long 755s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '28' because it was < 2 characters long 755s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '37' because it was < 2 characters long 755s 44 reads; of these: 755s 44 (100.00%) were unpaired; of these: 755s 44 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 0.00% overall alignment rate 755s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 755s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 755s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.2 755s Introducing 4 SNPs, 1/1 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.1 755s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 4 755s Reference gaps introduced: 2 755s Read gaps introduced: 1 755s Rearrangements introduced: 0 755s Created read sampler 755s Sampling 158 reads 755s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 755s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 755s *** Run 85 of 100 755s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 0.0217844987528782,0.049562930927076 --trim5 2 -N 1 -L28 --mp 9.43004350343426,4.20765597077588 --large-index --np 3 --cp-min 8 --rdg 32.1874141003612 --score-min L,2.35093164249751,9.0885277695604 -D 37 --gbar 1 -k 4 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 755s parsing sequence Sim.pm.1... 755s parsing sequence Sim.pm.2... 755s Parsed 166 reference bases 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 755s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '12' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 755s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '23' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 755s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #2 of read '27' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 755s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '31' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 755s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '35' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 755s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '36' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 755s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '37' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 755s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '48' because it was < 2 characters long 755s Read 50 alignments... 755s Read 100 alignments... 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 755s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #2 of read '56' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 755s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '65' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 755s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '67' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 755s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '80' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 755s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '86' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 755s Read 150 alignments... 755s Read 200 alignments... 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 755s Warning: skipping mate #1 of read '99' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '99' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 755s Warning: skipping mate #1 of read '100' because length (1) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '100' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 755s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '108' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 755s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '118' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 755s Read 250 alignments... 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 755s Warning: skipping mate #1 of read '154' because length (0) <= # seed mismatches (1) 755s Warning: skipping mate #1 of read '154' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 755s Read 300 alignments... 755s 158 reads; of these: 755s 148 (93.67%) were paired; of these: 755s 148 (100.00%) aligned concordantly 0 times 755s 0 (0.00%) aligned concordantly exactly 1 time 755s 0 (0.00%) aligned concordantly >1 times 755s ---- 755s 148 pairs aligned concordantly 0 times; of these: 755s 0 (0.00%) aligned discordantly 1 time 755s ---- 755s 148 pairs aligned 0 times concordantly or discordantly; of these: 755s 296 mates make up the pairs; of these: 755s 246 (83.11%) aligned 0 times 755s 11 (3.72%) aligned exactly 1 time 755s 39 (13.18%) aligned >1 times 755s 10 (6.33%) were unpaired; of these: 755s 8 (80.00%) aligned 0 times 755s 1 (10.00%) aligned exactly 1 time 755s 1 (10.00%) aligned >1 times 755s 16.99% overall alignment rate 755s Read 350 alignments... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CGGTTGCTTTAGG 755s CGGTTGCTTTAGG 755s Processing line... 755s CGGTTGCTTTAGG 755s CGGTTGCTTTAGG 755s Processing line... 755s CGGTTGCTTTAGG 755s CGGTTGCTTTAGG 755s Processing line... 755s Processing line... 755s GTTGCT 755s GTTGCT 755s Processing line... 755s GTTGCT 755s GTTGCT 755s Processing line... 755s GTTGCT 755s GTTGCT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CGGG 755s CGGG 755s Processing line... 755s CGGG 755s CGGG 755s Processing line... 755s CGGG 755s CGGG 755s Processing line... 755s CGGG 755s CGGG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGG 755s GTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGG 755s Processing line... 755s Processing line... 755s Processing line... 755s GGCGGTCTGAG 755s GGCGGTCTGAG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GGGGCGGCGG 755s GGGGCGGCGG 755s Processing line... 755s GGGGCGGCGG 755s GGGGCGGCGG 755s Processing line... 755s GGGGCGGCGG 755s GGGGCGGCGG 755s Processing line... 755s Processing line... 755s GCGG 755s GCGG 755s Processing line... 755s GCGG 755s GCGG 755s Processing line... 755s GCGG 755s GCGG 755s Processing line... 755s GCGG 755s GCGG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GGCCGG 755s GGCCGG 755s Processing line... 755s GGCCGG 755s GGCCGG 755s Processing line... 755s GGCCGG 755s GGCCGG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CGGTTGCTTTAGGA 755s CGGTTGCTTTAGGA 755s Processing line... 755s CGGTTGCTTTAGGA 755s CGGTTGCTTTAGGA 755s Processing line... 755s CGGTTGCTTTAGGA 755s CGGTTGCTTTAGGA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GATGGGCCGGGGC 755s GATGGGCCGGGGC 755s Processing line... 755s GATGGGCCGGGGC 755s GATGGGCCGGGGC 755s Processing line... 755s Processing line... 755s CTTTCGGGTGTCATTGTAGTGGCGGTCT 755s CTTTCGGGTGTCATTGTAGTGGCGGTCT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TTAG 755s TTAG 755s Processing line... 755s TTAG 755s TTAG 755s Processing line... 755s TTAG 755s TTAG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TGTAGTGGCGGTCTGAGGC 755s TGTAGTGGCGGTCTGAGGC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GCG 755s GCG 755s Processing line... 755s GCG 755s GCG 755s Processing line... 755s GCG 755s GCG 755s Processing line... 755s GCG 755s GCG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GC 755s GC 755s Processing line... 755s GC 755s GC 755s Processing line... 755s GC 755s GC 755s Processing line... 755s GC 755s GC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GGTTGCTTTAGGAGGGATGGGC 755s GGTTGCTTTAGGAGGGATGGGC 755s Processing line... 755s GGTTGCTTTAGGAGGGATGGGC 755s GGTTGCTTTAGGAGGGATGGGC 755s Processing line... 755s Processing line... 755s TCGGGTGTC 755s TCGGGTGTC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CGGT 755s CGGT 755s Processing line... 755s CGGT 755s CGGT 755s Processing line... 755s CGGT 755s CGGT 755s Processing line... 755s CGGT 755s CGGT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CGGGGCGGCGGTT 755s CGGGGCGGCGGTT 755s Processing line... 755s CGGGGCGGCGGTT 755s CGGGGCGGCGGTT 755s Processing line... 755s CGGGGCGGCGGTT 755s CGGGGCGGCGGTT 755s Processing line... 755s Processing line... 755s Processing line... 755s TGGGCGGTTGA 755s TGGGCGGTTGA 755s Processing line... 755s TGGGCGGTTGA 755s TGGGCGGTTGA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GTGTCATTGT 755s GTGTCATTGT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TT 755s TT 755s Processing line... 755s TT 755s TT 755s Processing line... 755s TT 755s TT 755s Processing line... 755s TT 755s TT 755s Processing line... 755s Processing line... 755s TCGG 755s TCGG 755s Processing line... 755s TCGG 755s TCGG 755s Processing line... 755s TCGG 755s TCGG 755s Processing line... 755s Processing line... 755s GCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGG 755s GCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGG 755s Processing line... 755s GCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGG 755s GCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GGAGGGATGGGCCGGGGCG 755s GGAGGGATGGGCCGGGGCG 755s Processing line... 755s GGAGGGATGGGCCGGGGCG 755s GGAGGGATGGGCCGGGGCG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GATGGGCCGGGGCGGC 755s GATGGGCCGGGGCGGC 755s Processing line... 755s GATGGGCCGGGGCGGC 755s GATGGGCCGGGGCGGC 755s Processing line... 755s Processing line... 755s GGTCTGA 755s GGTCTGA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s AGGGATGGGC 755s AGGGATGGGC 755s Processing line... 755s AGGGATGGGC 755s AGGGATGGGC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CTT 755s CTT 755s Processing line... 755s CTT 755s CTT 755s Processing line... 755s CTT 755s CTT 755s Processing line... 755s CTT 755s CTT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GAGGGA 755s GAGGGA 755s Processing line... 755s GAGGGA 755s GAGGGA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TT 755s TT 755s Processing line... 755s TT 755s TT 755s Processing line... 755s TT 755s TT 755s Processing line... 755s TT 755s TT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TCGGGA 755s TCGGGA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GCCGGGGCGGCGGTTGCTTTAGGAGG 755s GCCGGGGCGGCGGTTGCTTTAGGAGG 755s Processing line... 755s GCCGGGGCGGCGGTTGCTTTAGGAGG 755s GCCGGGGCGGCGGTTGCTTTAGGAGG 755s Processing line... 755s Processing line... 755s GGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGG 755s GGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGG 755s Processing line... 755s Processing line... 755s TTAG 755s TTAG 755s Processing line... 755s TTAG 755s TTAG 755s Processing line... 755s TTAG 755s TTAG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGC 755s GGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGC 755s Processing line... 755s Processing line... 755s GGAGGGAT 755s GGAGGGAT 755s Processing line... 755s GGAGGGAT 755s GGAGGGAT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GGG 755s GGG 755s Processing line... 755s GGG 755s GGG 755s Processing line... 755s GGG 755s GGG 755s Processing line... 755s GGG 755s GGG 755s Processing line... 755s Processing line... 755s GGGCCGG 755s GGGCCGG 755s Processing line... 755s GGGCCGG 755s GGGCCGG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CG 755s CG 755s Processing line... 755s CG 755s CG 755s Processing line... 755s CG 755s CG 755s Processing line... 755s CG 755s CG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CG 755s CG 755s Processing line... 755s CG 755s CG 755s Processing line... 755s CG 755s CG 755s Processing line... 755s CG 755s CG 755s Processing line... 755s Processing line... 755s ATGGG 755s ATGGG 755s Processing line... 755s ATGGG 755s ATGGG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TGGGCCGGGGCGGCG 755s TGGGCCGGGGCGGCG 755s Processing line... 755s TGGGCCGGGGCGGCG 755s TGGGCCGGGGCGGCG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GGT 755s GGT 755s Processing line... 755s GGT 755s GGT 755s Processing line... 755s GGT 755s GGT 755s Processing line... 755s GGT 755s GGT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s AGGGATGGGCCGGGGCGGCGGTTGCTTTA 755s AGGGATGGGCCGGGGCGGCGGTTGCTTTA 755s Processing line... 755s AGGGATGGGCCGGGGCGGCGGTTGCTTTA 755s AGGGATGGGCCGGGGCGGCGGTTGCTTTA 755s Processing line... 755s Processing line... 755s TAGTGGCGGTCTGAG 755s TAGTGGCGGTCTGAG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GT 755s GT 755s Processing line... 755s GT 755s GT 755s Processing line... 755s GT 755s GT 755s Processing line... 755s GT 755s GT 755s Processing line... 755s Processing line... 755s ATGGGCCGGGGCGGCGGTTGCTTTA 755s ATGGGCCGGGGCGGCGGTTGCTTTA 755s Processing line... 755s ATGGGCCGGGGCGGCGGTTGCTTTA 755s ATGGGCCGGGGCGGCGGTTGCTTTA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGA 755s GAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s AGGAGGGA 755s AGGAGGGA 755s Processing line... 755s AGGAGGGA 755s AGGAGGGA 755s Processing line... 755s Processing line... 755s GG 755s GG 755s Processing line... 755s GG 755s GG 755s Processing line... 755s GG 755s GG 755s Processing line... 755s GG 755s GG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GATGGGCCGGGGCG 755s GATGGGCCGGGGCG 755s Processing line... 755s GATGGGCCGGGGCG 755s GATGGGCCGGGGCG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 129 alignments, 0 edits 755s --------------- 755s PASSED 755s ALSO checking that bowtie2 and bowtie2-align match up 755s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 0.0217844987528782,0.049562930927076 --trim5 2 -N 1 -L28 --mp 9.43004350343426,4.20765597077588 --large-index --np 3 --cp-min 8 --rdg 32.1874141003612 --score-min L,2.35093164249751,9.0885277695604 -D 37 --gbar 1 -k 4 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 756s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '12' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 756s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '23' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 756s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #2 of read '27' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 756s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '31' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 756s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '35' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 756s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '36' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 756s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '37' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 756s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '48' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 756s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #2 of read '56' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 756s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '65' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 756s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '67' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 756s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '80' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 756s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '86' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 756s Warning: skipping mate #1 of read '99' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '99' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 756s Warning: skipping mate #1 of read '100' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '100' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 756s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '108' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 756s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '118' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 756s Warning: skipping mate #1 of read '154' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '154' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 756s 158 reads; of these: 756s 148 (93.67%) were paired; of these: 756s 148 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 148 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 148 pairs aligned 0 times concordantly or discordantly; of these: 756s 296 mates make up the pairs; of these: 756s 246 (83.11%) aligned 0 times 756s 11 (3.72%) aligned exactly 1 time 756s 39 (13.18%) aligned >1 times 756s 10 (6.33%) were unpaired; of these: 756s 8 (80.00%) aligned 0 times 756s 1 (10.00%) aligned exactly 1 time 756s 1 (10.00%) aligned >1 times 756s 16.99% overall alignment rate 756s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 756s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 756s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 0.0217844987528782,0.049562930927076 --trim5 2 -N 1 -L28 --mp 9.43004350343426,4.20765597077588 --large-index --np 3 --cp-min 8 --rdg 32.1874141003612 --score-min L,2.35093164249751,9.0885277695604 -D 37 --gbar 1 -k 4 -r -p 4 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 756s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '12' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 756s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '35' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 756s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '36' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 756s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '37' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 756s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '48' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 756s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '65' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 756s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '67' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 756s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '23' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 756s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #2 of read '27' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 756s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '31' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 756s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '80' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 756s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #2 of read '56' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 756s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '86' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 756s Warning: skipping mate #1 of read '99' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '99' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 756s Warning: skipping mate #1 of read '100' because length (1) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '100' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 756s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '108' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 756s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '118' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 756s Warning: skipping mate #1 of read '154' because length (0) <= # seed mismatches (1) 756s Warning: skipping mate #1 of read '154' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 756s 158 reads; of these: 756s 148 (93.67%) were paired; of these: 756s 148 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 148 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 148 pairs aligned 0 times concordantly or discordantly; of these: 756s 296 mates make up the pairs; of these: 756s 246 (83.11%) aligned 0 times 756s 11 (3.72%) aligned exactly 1 time 756s 39 (13.18%) aligned >1 times 756s 10 (6.33%) were unpaired; of these: 756s 8 (80.00%) aligned 0 times 756s 1 (10.00%) aligned exactly 1 time 756s 1 (10.00%) aligned >1 times 756s 16.99% overall alignment rate 756s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 756s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 756s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 756s Flattened IUPAC characters 756s Mutating sequence Sim.pm.1 756s Introducing 6 SNPs, 4/3 ref/read gaps, and 1 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutating sequence Sim.pm.2 756s Introducing 16 SNPs, 2/3 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutated reference genome to subject genome 756s SNPs introduced: 22 756s Reference gaps introduced: 6 756s Read gaps introduced: 6 756s Rearrangements introduced: 1 756s Created read sampler 756s Sampling 57 reads 756s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 756s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 756s parsing sequence Sim.pm.1... 756s parsing sequence Sim.pm.2... 756s *** Run 86 of 100 756s /usr/bin/bowtie2 --trim5 9 --large-index --cp-min 3 --cp-ival 2 --local -k 3 -N 0 -L27 --mp 8.32854965232626,7.70822692206096 --score-min L,5.91307683224395,2.003066260489 --rfg 12.2261673678757,13.8959638840318 --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 756s Parsed 166 reference bases 756s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 756s 57 reads; of these: 756s 43 (75.44%) were paired; of these: 756s 43 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 43 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 43 pairs aligned 0 times concordantly or discordantly; of these: 756s 86 mates make up the pairs; of these: 756s 86 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 14 (24.56%) were unpaired; of these: 756s 14 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s Read 50 alignments... 756s Read 100 alignments... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s --- Summary --- 756s Read 1 reference strings 756s Checked 0 alignments, 0 edits 756s --------------- 756s PASSED 756s ALSO checking that bowtie2 and bowtie2-align match up 756s /usr/bin/bowtie2 --trim5 9 --large-index --cp-min 3 --cp-ival 2 --local -k 3 -N 0 -L27 --mp 8.32854965232626,7.70822692206096 --score-min L,5.91307683224395,2.003066260489 --rfg 12.2261673678757,13.8959638840318 --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 756s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 756s 57 reads; of these: 756s 43 (75.44%) were paired; of these: 756s 43 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 43 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 43 pairs aligned 0 times concordantly or discordantly; of these: 756s 86 mates make up the pairs; of these: 756s 86 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 14 (24.56%) were unpaired; of these: 756s 14 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 756s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 756s /usr/bin/bowtie2 --trim5 9 --large-index --cp-min 3 --cp-ival 2 --local -k 3 -N 0 -L27 --mp 8.32854965232626,7.70822692206096 --score-min L,5.91307683224395,2.003066260489 --rfg 12.2261673678757,13.8959638840318 --qseq -p 2 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 756s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 756s 57 reads; of these: 756s 43 (75.44%) were paired; of these: 756s 43 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 43 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 43 pairs aligned 0 times concordantly or discordantly; of these: 756s 86 mates make up the pairs; of these: 756s 86 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 14 (24.56%) were unpaired; of these: 756s 14 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 756s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 756s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 756s /usr/bin/bowtie2 --trim5 9 --large-index --cp-min 3 --cp-ival 2 --local -k 3 -N 0 -L27 --mp 8.32854965232626,7.70822692206096 --score-min L,5.91307683224395,2.003066260489 --rfg 12.2261673678757,13.8959638840318 --qseq -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 756s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 756s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 756s 57 reads; of these: 756s 43 (75.44%) were paired; of these: 756s 43 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 43 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 43 pairs aligned 0 times concordantly or discordantly; of these: 756s 86 mates make up the pairs; of these: 756s 86 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 14 (24.56%) were unpaired; of these: 756s 14 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 756s Flattened IUPAC characters 756s Mutating sequence Sim.pm.2 756s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutating sequence Sim.pm.1 756s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutated reference genome to subject genome 756s SNPs introduced: 10 756s Reference gaps introduced: 1 756s Read gaps introduced: 0 756s Rearrangements introduced: 0 756s Created read sampler 756s Sampling 68 reads 756s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 756s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 756s parsing sequence Sim.pm.1... 756s parsing sequence Sim.pm.2... 756s Parsed 166 reference bases 756s *** Run 87 of 100 756s /usr/bin/bowtie2 --norc --n-ceil 1.33634145445611,1.30313502590474 --cp-ival 2 --trim3 2 --nofw -i S,1.87375796831652,2.42853837992333 --mp 8.30454548163636,6.97870586355682 -N 1 -L25 --large-index --np 3 --cp-min 2 --score-min L,7.04153997755186,3.78887156306491 --ma 22.5530338007993 -k 2 -D 5 --mm -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 757s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 757s Warning: skipping mate #2 of read '0' because length (1) <= # seed mismatches (1) 757s Warning: skipping mate #2 of read '0' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 757s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (1) 757s Warning: skipping mate #1 of read '2' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 757s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (1) 757s Warning: skipping mate #1 of read '13' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 757s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (1) 757s Warning: skipping mate #1 of read '25' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 757s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (1) 757s Warning: skipping mate #2 of read '45' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 757s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (1) 757s Warning: skipping mate #1 of read '59' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 757s Read 50 alignments... 757s Read 100 alignments... 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 757s 68 reads; of these: 757s 60 (88.24%) were paired; of these: 757s 60 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 60 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 60 pairs aligned 0 times concordantly or discordantly; of these: 757s 120 mates make up the pairs; of these: 757s 120 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 8 (11.76%) were unpaired; of these: 757s 8 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 0 alignments, 0 edits 757s --------------- 757s PASSED 757s ALSO checking that bowtie2 and bowtie2-align match up 757s /usr/bin/bowtie2 --norc --n-ceil 1.33634145445611,1.30313502590474 --cp-ival 2 --trim3 2 --nofw -i S,1.87375796831652,2.42853837992333 --mp 8.30454548163636,6.97870586355682 -N 1 -L25 --large-index --np 3 --cp-min 2 --score-min L,7.04153997755186,3.78887156306491 --ma 22.5530338007993 -k 2 -D 5 --mm -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 757s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 757s Warning: skipping mate #2 of read '0' because length (1) <= # seed mismatches (1) 757s Warning: skipping mate #2 of read '0' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 757s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (1) 757s Warning: skipping mate #1 of read '2' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 757s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (1) 757s Warning: skipping mate #1 of read '13' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 757s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (1) 757s Warning: skipping mate #1 of read '25' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 757s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (1) 757s Warning: skipping mate #2 of read '45' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 757s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (1) 757s Warning: skipping mate #1 of read '59' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 757s 68 reads; of these: 757s 60 (88.24%) were paired; of these: 757s 60 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 60 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 60 pairs aligned 0 times concordantly or discordantly; of these: 757s 120 mates make up the pairs; of these: 757s 120 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 8 (11.76%) were unpaired; of these: 757s 8 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 757s Flattened IUPAC characters 757s Mutating sequence Sim.pm.2 757s Introducing 23 SNPs, 0/0 ref/read gaps, and 2 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutating sequence Sim.pm.1 757s Introducing 25 SNPs, 1/1 ref/read gaps, and 3 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutated reference genome to subject genome 757s SNPs introduced: 48 757s Reference gaps introduced: 1 757s Read gaps introduced: 1 757s Rearrangements introduced: 5 757s Created read sampler 757s Sampling 6 reads 757s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 757s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 757s parsing sequence Sim.pm.1... 757s parsing sequence Sim.pm.2... 757s *** Run 88 of 100 757s /usr/bin/bowtie2 --rdg 7.44965162836965 --score-min L,2.79560274194285,7.25418292666113 -D 6 --large-index --cp-min 5 --mp 7.27778624957978,5.01638308372002 --local --cp-ival 1 -M 2 --trim5 0 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta 757s Parsed 166 reference bases 757s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 757s 6 reads; of these: 757s 6 (100.00%) were unpaired; of these: 757s 6 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s /usr/bin/bowtie2 --rdg 7.44965162836965 --score-min L,2.79560274194285,7.25418292666113 -D 6 --large-index --cp-min 5 --mp 7.27778624957978,5.01638308372002 --local --cp-ival 1 -M 2 --trim5 0 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 0 alignments, 0 edits 757s --------------- 757s PASSED 757s ALSO checking that bowtie2 and bowtie2-align match up 757s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 757s 6 reads; of these: 757s 6 (100.00%) were unpaired; of these: 757s 6 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 757s Flattened IUPAC characters 757s Mutating sequence Sim.pm.1 757s *** Run 89 of 100 757s /usr/bin/bowtie2 -i C,3.65308102244134,11.4067687306438 --score-min L,5.96948510241054,3.95321730525395 --nofw --cp-ival 2 --local --trim5 8 --large-index -M 6 --cp-min 4 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 757s Introducing 25 SNPs, 0/1 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutating sequence Sim.pm.2 757s Introducing 19 SNPs, 1/0 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutated reference genome to subject genome 757s SNPs introduced: 44 757s Reference gaps introduced: 1 757s Read gaps introduced: 1 757s Rearrangements introduced: 0 757s Created read sampler 757s Sampling 262 reads 757s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 757s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 757s parsing sequence Sim.pm.1... 757s parsing sequence Sim.pm.2... 757s Parsed 166 reference bases 757s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 757s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '4' because it was < 2 characters long 757s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '8' because it was < 2 characters long 757s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '11' because it was < 2 characters long 757s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '13' because it was < 2 characters long 757s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '16' because it was < 2 characters long 757s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '27' because it was < 2 characters long 757s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '41' because it was < 2 characters long 757s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '50' because it was < 2 characters long 757s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '52' because it was < 2 characters long 757s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '65' because it was < 2 characters long 757s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '66' because it was < 2 characters long 757s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '67' because it was < 2 characters long 757s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '68' because it was < 2 characters long 757s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '75' because it was < 2 characters long 757s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '78' because it was < 2 characters long 757s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '79' because it was < 2 characters long 757s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '80' because it was < 2 characters long 757s Read 50 alignments... 757s Read 100 alignments... 757s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '86' because it was < 2 characters long 757s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '89' because it was < 2 characters long 757s Warning: skipping mate #2 of read '90' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '90' because it was < 2 characters long 757s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '93' because it was < 2 characters long 757s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '95' because it was < 2 characters long 757s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '97' because it was < 2 characters long 757s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '102' because it was < 2 characters long 757s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '112' because it was < 2 characters long 757s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '113' because it was < 2 characters long 757s Warning: skipping mate #1 of read '116' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '116' because it was < 2 characters long 757s Warning: skipping mate #1 of read '136' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '136' because it was < 2 characters long 757s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '137' because it was < 2 characters long 757s Warning: skipping mate #1 of read '139' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '139' because it was < 2 characters long 757s Warning: skipping mate #1 of read '141' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '141' because it was < 2 characters long 757s Read 150 alignments... 757s Warning: skipping mate #1 of read '162' because length (0) <= # seed mismatches (0) 757s Read 200 alignments... 757s Warning: skipping mate #1 of read '162' because it was < 2 characters long 757s Warning: skipping mate #1 of read '166' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '166' because it was < 2 characters long 757s Warning: skipping mate #1 of read '170' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '170' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '170' because it was < 2 characters long 757s Warning: skipping mate #2 of read '170' because it was < 2 characters long 757s Warning: skipping mate #1 of read '172' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '172' because it was < 2 characters long 757s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '178' because it was < 2 characters long 757s Warning: skipping mate #1 of read '180' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '180' because it was < 2 characters long 757s Warning: skipping mate #1 of read '184' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '184' because it was < 2 characters long 757s Warning: skipping mate #1 of read '190' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '190' because it was < 2 characters long 757s Warning: skipping mate #1 of read '192' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '192' because it was < 2 characters long 757s Warning: skipping mate #1 of read '195' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '195' because it was < 2 characters long 757s Warning: skipping mate #2 of read '196' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '196' because it was < 2 characters long 757s Warning: skipping mate #1 of read '201' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '201' because it was < 2 characters long 757s Warning: skipping mate #1 of read '203' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '203' because it was < 2 characters long 757s Warning: skipping mate #1 of read '207' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '207' because it was < 2 characters long 757s Warning: skipping read '213' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '213' because it was < 2 characters long 757s Warning: skipping mate #1 of read '214' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '214' because it was < 2 characters long 757s Warning: skipping read '217' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '217' because it was < 2 characters long 757s Warning: skipping read '228' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '228' because it was < 2 characters long 757s Warning: skipping mate #1 of read '236' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '236' because it was < 2 characters long 757s Warning: skipping mate #1 of read '238' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '238' because it was < 2 characters long 757s Warning: skipping read '239' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '239' because it was < 2 characters long 757s Read 250 alignments... 757s Warning: skipping mate #1 of read '245' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '245' because it was < 2 characters long 757s Warning: skipping mate #1 of read '254' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '254' because it was < 2 characters long 757s Warning: skipping mate #1 of read '256' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '256' because it was < 2 characters long 757s Read 300 alignments... 757s 262 reads; of these: 757s 216 (82.44%) were paired; of these: 757s 216 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 216 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 216 pairs aligned 0 times concordantly or discordantly; of these: 757s 432 mates make up the pairs; of these: 757s 432 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 46 (17.56%) were unpaired; of these: 757s 46 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s Read 350 alignments... 757s Read 400 alignments... 757s Read 450 alignments... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 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Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing 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Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 0 alignments, 0 edits 757s --------------- 757s PASSED 757s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 757s /usr/bin/bowtie2 -i C,3.65308102244134,11.4067687306438 --score-min L,5.96948510241054,3.95321730525395 --nofw --cp-ival 2 --local --trim5 8 --large-index -M 6 --cp-min 4 -q -p 4 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 757s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 757s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '4' because it was < 2 characters long 757s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '8' because it was < 2 characters long 757s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '11' because it was < 2 characters long 757s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '13' because it was < 2 characters long 757s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '16' because it was < 2 characters long 757s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '27' because it was < 2 characters long 757s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '41' because it was < 2 characters long 757s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '50' because it was < 2 characters long 757s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '52' because it was < 2 characters long 757s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '65' because it was < 2 characters long 757s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '66' because it was < 2 characters long 757s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '67' because it was < 2 characters long 757s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '68' because it was < 2 characters long 757s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '75' because it was < 2 characters long 757s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '78' because it was < 2 characters long 757s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '79' because it was < 2 characters long 757s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '80' because it was < 2 characters long 757s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '86' because it was < 2 characters long 757s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '89' because it was < 2 characters long 757s Warning: skipping mate #2 of read '90' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '90' because it was < 2 characters long 757s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '93' because it was < 2 characters long 757s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '95' because it was < 2 characters long 757s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '97' because it was < 2 characters long 757s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '102' because it was < 2 characters long 757s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '112' because it was < 2 characters long 757s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '113' because it was < 2 characters long 757s Warning: skipping mate #1 of read '116' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '116' because it was < 2 characters long 757s Warning: skipping mate #1 of read '136' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '136' because it was < 2 characters long 757s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '137' because it was < 2 characters long 757s Warning: skipping mate #1 of read '139' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '139' because it was < 2 characters long 757s Warning: skipping mate #1 of read '141' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '141' because it was < 2 characters long 757s Warning: skipping mate #1 of read '162' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '162' because it was < 2 characters long 757s Warning: skipping mate #1 of read '166' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '166' because it was < 2 characters long 757s Warning: skipping mate #1 of read '170' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '170' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '170' because it was < 2 characters long 757s Warning: skipping mate #2 of read '170' because it was < 2 characters long 757s Warning: skipping mate #1 of read '172' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '172' because it was < 2 characters long 757s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '178' because it was < 2 characters long 757s Warning: skipping mate #1 of read '180' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '180' because it was < 2 characters long 757s Warning: skipping mate #1 of read '184' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '184' because it was < 2 characters long 757s Warning: skipping mate #1 of read '190' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '190' because it was < 2 characters long 757s Warning: skipping mate #1 of read '192' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '192' because it was < 2 characters long 757s Warning: skipping mate #1 of read '195' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '195' because it was < 2 characters long 757s Warning: skipping mate #2 of read '196' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '196' because it was < 2 characters long 757s Warning: skipping mate #1 of read '201' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '201' because it was < 2 characters long 757s Warning: skipping mate #1 of read '203' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '203' because it was < 2 characters long 757s Warning: skipping mate #1 of read '207' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '207' because it was < 2 characters long 757s Warning: skipping read '213' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '213' because it was < 2 characters long 757s Warning: skipping mate #1 of read '214' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '214' because it was < 2 characters long 757s Warning: skipping read '217' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '217' because it was < 2 characters long 757s Warning: skipping read '228' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '228' because it was < 2 characters long 757s Warning: skipping mate #1 of read '236' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '236' because it was < 2 characters long 757s Warning: skipping mate #1 of read '238' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '238' because it was < 2 characters long 757s Warning: skipping read '239' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '239' because it was < 2 characters long 757s Warning: skipping mate #1 of read '245' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '245' because it was < 2 characters long 757s Warning: skipping mate #1 of read '254' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '254' because it was < 2 characters long 757s Warning: skipping mate #1 of read '256' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '256' because it was < 2 characters long 757s 262 reads; of these: 757s 216 (82.44%) were paired; of these: 757s 216 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 216 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 216 pairs aligned 0 times concordantly or discordantly; of these: 757s 432 mates make up the pairs; of these: 757s 432 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 46 (17.56%) were unpaired; of these: 757s 46 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 757s Flattened IUPAC characters 757s Mutating sequence Sim.pm.1 757s Introducing 5 SNPs, 1/1 ref/read gaps, and 3 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutating sequence Sim.pm.2 757s Introducing 11 SNPs, 0/2 ref/read gaps, and 1 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutated reference genome to subject genome 757s SNPs introduced: 16 757s Reference gaps introduced: 1 757s Read gaps introduced: 3 757s Rearrangements introduced: 4 757s Created read sampler 757s Sampling 143 reads 757s *** Run 90 of 100 757s /usr/bin/bowtie2 --mm --ma 29.9858995446942 --score-min L,6.79798472757857,2.95229537875629 --mp 7.30573282343675,1.36808740733537 --cp-ival 1 --cp-min 10 --large-index -M 4 --norc --qseq -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq 757s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 757s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 757s parsing sequence Sim.pm.1... 757s parsing sequence Sim.pm.2... 757s Parsed 166 reference bases 757s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 757s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 757s Read 50 alignments... 757s Read 100 alignments... 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_122_122_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 757s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 757s 143 reads; of these: 757s 143 (100.00%) were paired; of these: 757s 143 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 143 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 143 pairs aligned 0 times concordantly or discordantly; of these: 757s 286 mates make up the pairs; of these: 757s 258 (90.21%) aligned 0 times 757s 3 (1.05%) aligned exactly 1 time 757s 25 (8.74%) aligned >1 times 757s 9.79% overall alignment rate 757s Read 150 alignments... 757s Read 200 alignments... 757s Read 250 alignments... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGGATGGGCCGGGGCGGCG 757s GGGATGGGCCGGGGCGGCG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CT 757s CT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGGTGTCATTGTAGTGGCGG 757s GGGTGTCATTGTAGTGGCGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GC 757s GC 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s TAGG 757s TAGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s TGTAGT 757s TGTAGT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s ACT 757s ACT 757s Processing line... 757s GAGGG 757s GAGGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GATGGGCCGGGGCGGCGGTTGCTTTAGGAGG 757s GATGGGCCGGGGCGGCGGTTGCTTTAGGAGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s AGGAGGGATGGGCCGGGGCGG 757s AGGAGGGATGGGCCGGGGCGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s AGGGATGGGCCGGGGCGGCGG 757s AGGGATGGGCCGGGGCGGCGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGGATG 757s GGGATG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CC 757s CC 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GT 757s GT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s AGGG 757s AGGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGA 757s GGA 757s Processing line... 757s Processing line... 757s TGG 757s TGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGGGCGGCGG 757s GGGGCGGCGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s AC 757s AC 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGC 757s CGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTGC 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CG 757s CG 757s Processing line... 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CG 757s CG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s TTCG 757s TTCG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGG 757s GGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s TGATCGGGAGT 757s TGATCGGGAGT 757s Processing line... 757s Processing line... 757s GA 757s GA 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s TTTAGGAGGG 757s TTTAGGAGGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 28 alignments, 0 edits 757s --------------- 757s PASSED 757s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 757s /usr/bin/bowtie2 --mm --ma 29.9858995446942 --score-min L,6.79798472757857,2.95229537875629 --mp 7.30573282343675,1.36808740733537 --cp-ival 1 --cp-min 10 --large-index -M 4 --norc --qseq -p 2 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.qseq -2 /tmp/Sim.pm.pBDT5Pxz_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 757s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 757s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_122_122_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 757s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 757s Warning: skipping mate #2 of read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 757s 143 reads; of these: 757s 143 (100.00%) were paired; of these: 757s 143 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 143 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 143 pairs aligned 0 times concordantly or discordantly; of these: 757s 286 mates make up the pairs; of these: 757s 258 (90.21%) aligned 0 times 757s 3 (1.05%) aligned exactly 1 time 757s 25 (8.74%) aligned >1 times 757s 9.79% overall alignment rate 757s Flattened IUPAC characters 757s Mutating sequence Sim.pm.1 757s Introducing 10 SNPs, 5/2 ref/read gaps, and 3 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 757s *** Run 91 of 100 757s /usr/bin/bowtie2 --mm --ma 17.6925152222923 --score-min L,7.60633114703845,8.22948654997459 -R 1 --np 3 --cp-min 3 --large-index --trim3 5 -i S,1.68478357289294 --cp-ival 1 -a --trim5 5 --n-ceil 0.543949856998277,0.920973380693578 -q -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fastq 757s Finished read gaps 757s Mutating sequence Sim.pm.2 757s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutated reference genome to subject genome 757s SNPs introduced: 11 757s Reference gaps introduced: 6 757s Read gaps introduced: 2 757s Rearrangements introduced: 3 757s Created read sampler 757s Sampling 174 reads 757s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 757s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 757s parsing sequence Sim.pm.1... 757s parsing sequence Sim.pm.2... 757s Parsed 166 reference bases 757s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 757s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 757s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read '1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 757s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '4' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 757s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '10' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 757s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '11' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 757s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '12' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 757s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '15' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 757s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '18' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 757s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '29' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 757s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '30' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 757s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '31' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 757s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '32' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 757s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '35' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 757s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '39' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 757s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '42' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 757s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '44' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 757s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '45' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 757s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '47' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 757s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '52' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 757s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '56' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 757s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '57' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 757s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 757s Warning: skipping read '59' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 757s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '65' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 757s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '72' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 757s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '77' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 757s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '79' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 757s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '85' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 757s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '100' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 757s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '104' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 757s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '105' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 757s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '106' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 757s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '108' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 757s Warning: skipping read '109' because length (1) <= # seed mismatches (0) 757s Warning: skipping read '109' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 757s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '110' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 757s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '111' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 757s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '114' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 757s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '115' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 757s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '116' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 757s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '127' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 757s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '131' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 757s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '133' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 757s Warning: skipping read '139' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '139' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 757s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '143' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 757s Warning: skipping read '145' because length (1) <= # seed mismatches (0) 757s Warning: skipping read '145' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 757s Warning: skipping read '148' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '148' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 757s Warning: skipping read '150' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '150' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 757s Warning: skipping read '151' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '151' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 757s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '154' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 757s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '156' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 757s Warning: skipping read '157' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '157' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 757s Warning: skipping read '159' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '159' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 757s Read 50 alignments... 757s Read 100 alignments... 757s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 757s Warning: skipping read '166' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '166' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 757s Warning: skipping read '170' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '170' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 757s Warning: skipping read '173' because length (1) <= # seed mismatches (0) 757s Warning: skipping read '173' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 757s 174 reads; of these: 757s 174 (100.00%) were unpaired; of these: 757s 147 (84.48%) aligned 0 times 757s 7 (4.02%) aligned exactly 1 time 757s 20 (11.49%) aligned >1 times 757s 15.52% overall alignment rate 757s Read 150 alignments... 757s Read 200 alignments... 757s Read 250 alignments... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGTTGA 757s GGTTGA 757s Processing line... 757s GGTTGA 757s GGTTGA 757s Processing line... 757s Processing line... 757s Processing line... 757s TGG 757s TGG 757s Processing line... 757s TGG 757s TGG 757s Processing line... 757s TGG 757s TGG 757s Processing line... 757s TGG 757s TGG 757s Processing line... 757s TGG 757s TGG 757s Processing line... 757s GGTTGA 757s GGTTGA 757s Processing line... 757s GGTTGA 757s GGTTGA 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGGCCGG 757s GGGCCGG 757s Processing line... 757s GGGCCGG 757s GGGCCGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GAGTGGG 757s GAGTGGG 757s Processing line... 757s GGTTGCTTTAGGAGGGATGGGC 757s GGTTGCTTTAGGAGGGATGGGC 757s Processing line... 757s GGTTGCTTTAGGAGGGATGGGC 757s GGTTGCTTTAGGAGGGATGGGC 757s Processing line... 757s Processing line... 757s TCAT 757s TCAT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CCG 757s CCG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CCG 757s CCG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CCG 757s CCG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s CGG 757s CGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s TAGGAGGGATGGGC 757s TAGGAGGGATGGGC 757s Processing line... 757s TAGGAGGGATGGGC 757s TAGGAGGGATGGGC 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGATGGGCCGGGGC 757s GGATGGGCCGGGGC 757s Processing line... 757s GGATGGGCCGGGGC 757s GGATGGGCCGGGGC 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s TCGGGAGTGGGCGGTTGACTTT 757s TCGGGAGTGGGCGGTTGACTTT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s CC 757s CC 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s CC 757s CC 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s CC 757s CC 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GG 757s GG 757s Processing line... 757s GGCG 757s GGCG 757s Processing line... 757s GGCG 757s GGCG 757s Processing line... 757s GGCG 757s GGCG 757s Processing line... 757s GGCG 757s GGCG 757s Processing line... 757s GGCG 757s GGCG 757s Processing line... 757s GGCG 757s GGCG 757s Processing line... 757s GGCG 757s GGCG 757s Processing line... 757s GGCG 757s GGCG 757s Processing line... 757s GGCG 757s GGCG 757s Processing line... 757s GGCG 757s GGCG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CCGGGGCGGCGGTT 757s CCGGGGCGGCGGTT 757s Processing line... 757s CCGGGGCGGCGGTT 757s CCGGGGCGGCGGTT 757s Processing line... 757s Processing line... 757s TTTAGGAG 757s TTTAGGAG 757s Processing line... 757s TTTAGGAG 757s TTTAGGAG 757s Processing line... 757s TTTAGGAG 757s TTTAGGAG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CTTTAGGAGGGATGGGCCGGGGCGGCGGTTG 757s CTTTAGGAGGGATGGGCCGGGGCGGCGGTTG 757s Processing line... 757s CTTTAGGAGGGATGGGCCGGGGCGGCGGTTG 757s CTTTAGGAGGGATGGGCCGGGGCGGCGGTTG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s TTGCT 757s TTGCT 757s Processing line... 757s TTGCT 757s TTGCT 757s Processing line... 757s TTGCT 757s TTGCT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CTTTAGGAGGGATGG 757s CTTTAGGAGGGATGG 757s Processing line... 757s CTTTAGGAGGGATGG 757s CTTTAGGAGGGATGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s ACT 757s ACT 757s Processing line... 757s ACT 757s ACT 757s Processing line... 757s AGT 757s AGT 757s Processing line... 757s AGT 757s AGT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GATCGGGAGTGGGCGGTTGACTTT 757s GATCGGGAGTGGGCGGTTGACTTT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGCC 757s GGCC 757s Processing line... 757s GGCC 757s GGCC 757s Processing line... 757s GGCC 757s GGCC 757s Processing line... 757s GGCC 757s GGCC 757s Processing line... 757s GGCC 757s GGCC 757s Processing line... 757s GGCC 757s GGCC 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GTTGACT 757s GTTGACT 757s Processing line... 757s GTTGACT 757s GTTGACT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGTTGCTTTA 757s GGTTGCTTTA 757s Processing line... 757s GGTTGCTTTA 757s GGTTGCTTTA 757s Processing line... 757s GGTTGCTTTA 757s GGTTGCTTTA 757s Processing line... 757s Processing line... 757s Processing line... 757s GATGGGCCG 757s GATGGGCCG 757s Processing line... 757s GATGGGCCG 757s GATGGGCCG 757s Processing line... 757s Processing line... 757s Processing line... 757s CGGGAGTGGGCGGTTGACTTTCG 757s CGGGAGTGGGCGGTTGACTTTCG 757s Processing line... 757s Processing line... 757s Processing line... 757s GTCT 757s GTCT 757s Processing line... 757s GGCGGTTGACTTTCGGGTGTCATTGTAGTGGCGGTC 757s GGCGGTTGACTTTCGGGTGTCATTGTAGTGGCGGTC 757s Processing line... 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 128 alignments, 0 edits 757s --------------- 757s PASSED 757s *** Run 92 of 100 757s /usr/bin/bowtie2 --score-min L,2.98701571249232,1.94212277703008 --nofw --gbar 1 --cp-ival 1 --large-index --cp-min 6 --np 6 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw 757s Flattened IUPAC characters 757s Mutating sequence Sim.pm.2 757s Introducing 15 SNPs, 0/0 ref/read gaps, and 1 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutating sequence Sim.pm.1 757s Introducing 17 SNPs, 0/0 ref/read gaps, and 3 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutated reference genome to subject genome 757s SNPs introduced: 32 757s Reference gaps introduced: 0 757s Read gaps introduced: 0 757s Rearrangements introduced: 4 757s Created read sampler 757s Sampling 74 reads 757s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 757s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 757s parsing sequence Sim.pm.1... 757s parsing sequence Sim.pm.2... 757s Parsed 166 reference bases 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 757s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '15' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 757s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '19' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 757s Read 50 alignments... 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 757s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '70' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 757s Read 100 alignments... 757s 74 reads; of these: 757s 74 (100.00%) were paired; of these: 757s 74 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 74 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 74 pairs aligned 0 times concordantly or discordantly; of these: 757s 148 mates make up the pairs; of these: 757s 139 (93.92%) aligned 0 times 757s 1 (0.68%) aligned exactly 1 time 757s 8 (5.41%) aligned >1 times 757s 6.08% overall alignment rate 757s Read 150 alignments... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CC 757s CC 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GTGGG 757s GTGGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGTTGCTTTAGGAGG 757s GGTTGCTTTAGGAGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GATGGGCCGGGGCGGCGGTTGCTTTA 757s GATGGGCCGGGGCGGCGGTTGCTTTA 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GAGG 757s GAGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s TGCTTTAGGAGGGATGGGCCGG 757s TGCTTTAGGAGGGATGGGCCGG 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GGCC 757s GGCC 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CC 757s CC 757s Processing line... 757s Processing line... 757s TGACTTTCG 757s TGACTTTCG 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 9 alignments, 0 edits 757s --------------- 757s PASSED 757s ALSO checking that bowtie2 and bowtie2-align match up 757s /usr/bin/bowtie2 --score-min L,2.98701571249232,1.94212277703008 --nofw --gbar 1 --cp-ival 1 --large-index --cp-min 6 --np 6 -r -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.raw -2 /tmp/Sim.pm.pBDT5Pxz_2.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 758s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #2 of read '15' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 758s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #2 of read '19' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 758s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '70' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 758s 74 reads; of these: 758s 74 (100.00%) were paired; of these: 758s 74 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 74 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 74 pairs aligned 0 times concordantly or discordantly; of these: 758s 148 mates make up the pairs; of these: 758s 139 (93.92%) aligned 0 times 758s 1 (0.68%) aligned exactly 1 time 758s 8 (5.41%) aligned >1 times 758s 6.08% overall alignment rate 758s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 758s Flattened IUPAC characters 758s Mutating sequence Sim.pm.1 758s Introducing 15 SNPs, 0/0 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutating sequence Sim.pm.2 758s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutated reference genome to subject genome 758s SNPs introduced: 17 758s Reference gaps introduced: 0 758s Read gaps introduced: 0 758s Rearrangements introduced: 0 758s Created read sampler 758s Sampling 167 reads 758s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 758s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 758s parsing sequence Sim.pm.1... 758s parsing sequence Sim.pm.2... 758s Parsed 166 reference bases 758s *** Run 93 of 100 758s /usr/bin/bowtie2 --nofw --mp 2.67181863594082,1.67268559624361 --rfg 10.9288202724185 --n-ceil 0.564297970601044,1.35455591121561 --trim5 6 --cp-ival 2 --score-min L,3.54952584752333,4.54184345670822 -R 3 -D 23 --rdg 42.4425412754603,6.08117560711686 --mm --cp-min 4 --large-index -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 758s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '15' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 758s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '26' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 758s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '30' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 758s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '49' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 758s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '53' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 758s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '60' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 758s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '61' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 758s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '64' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 758s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '74' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 758s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '76' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 758s Read 50 alignments... 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 758s Read 100 alignments... 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 758s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '92' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 758s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '97' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 758s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '98' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 758s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '101' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 758s Warning: skipping mate #1 of read '103' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '103' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 758s Warning: skipping mate #2 of read '106' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #2 of read '106' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 758s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '107' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 758s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '115' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 758s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '123' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 758s Warning: skipping mate #1 of read '140' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '140' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 758s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '144' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 758s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '151' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 758s Warning: skipping mate #1 of read '154' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '154' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 758s Read 150 alignments... 758s 167 reads; of these: 758s 142 (85.03%) were paired; of these: 758s 142 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 142 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 142 pairs aligned 0 times concordantly or discordantly; of these: 758s 284 mates make up the pairs; of these: 758s 262 (92.25%) aligned 0 times 758s 8 (2.82%) aligned exactly 1 time 758s 14 (4.93%) aligned >1 times 758s 25 (14.97%) were unpaired; of these: 758s 23 (92.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 2 (8.00%) aligned >1 times 758s 7.77% overall alignment rate 758s Read 200 alignments... 758s Read 250 alignments... 758s Read 300 alignments... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GGGTGTCATTGTAGTGGCGGTCTGAGGCCG 758s GGGTGTCATTGTAGTGGCGGTCTGAGGCCG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CCGG 758s CCGG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GGGGCGGCGGTTGC 758s GGGGCGGCGGTTGC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CGGG 758s CGGG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TG 758s TG 758s Processing line... 758s Processing line... 758s Processing line... 758s TGGGCCGGGGCGGCGGTTGC 758s TGGGCCGGGGCGGCGGTTGC 758s Processing line... 758s Processing line... 758s TTGACTTTC 758s TTGACTTTC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GC 758s GC 758s Processing line... 758s Processing line... 758s GTTGC 758s GTTGC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CTT 758s CTT 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s ATT 758s ATT 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CCGGGGCGGCGGTTGCTTTAGGAGGGATGGGC 758s CCGGGGCGGCGGTTGCTTTAGGAGGGATGGGC 758s Processing line... 758s Processing line... 758s Processing line... 758s /usr/bin/bowtie2 --nofw --mp 2.67181863594082,1.67268559624361 --rfg 10.9288202724185 --n-ceil 0.564297970601044,1.35455591121561 --trim5 6 --cp-ival 2 --score-min L,3.54952584752333,4.54184345670822 -R 3 -D 23 --rdg 42.4425412754603,6.08117560711686 --mm --cp-min 4 --large-index -f -p 3 -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GTGGCG 758s GTGGCG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TTGACTTTCGGGTGTCA 758s TTGACTTTCGGGTGTCA 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GCGGCGGTTGCTTTAG 758s GCGGCGGTTGCTTTAG 758s Processing line... 758s Processing line... 758s CGG 758s CGG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CT 758s CT 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CC 758s CC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CGGGAGTGGGCGGTTGACTTTCG 758s CGGGAGTGGGCGGTTGACTTTCG 758s Processing line... 758s Processing line... 758s Processing line... 758s GCTTT 758s GCTTT 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GGTTGACTTTCGGGTGTCATTGTAGT 758s GGTTGACTTTCGGGTGTCATTGTAGT 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GGGTGTCATTGTAGTGGCGGTC 758s GGGTGTCATTGTAGTGGCGGTC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TGC 758s TGC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CC 758s CC 758s Processing line... 758s --- Summary --- 758s Read 1 reference strings 758s Checked 24 alignments, 0 edits 758s --------------- 758s PASSED 758s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 758s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '15' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 758s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '26' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 758s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '30' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 758s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '49' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 758s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '53' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 758s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '60' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 758s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '61' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 758s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '64' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 758s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '74' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 758s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '76' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 758s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '97' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 758s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '98' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 758s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '101' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 758s Warning: skipping mate #1 of read '103' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '103' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 758s Warning: skipping mate #2 of read '106' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #2 of read '106' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 758s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '107' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 758s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '115' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 758s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '123' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 758s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '92' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 758s Warning: skipping mate #1 of read '140' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '140' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 758s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '144' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 758s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '151' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 758s Warning: skipping mate #1 of read '154' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '154' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 758s 167 reads; of these: 758s 142 (85.03%) were paired; of these: 758s 142 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 142 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 142 pairs aligned 0 times concordantly or discordantly; of these: 758s 284 mates make up the pairs; of these: 758s 262 (92.25%) aligned 0 times 758s 8 (2.82%) aligned exactly 1 time 758s 14 (4.93%) aligned >1 times 758s 25 (14.97%) were unpaired; of these: 758s 23 (92.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 2 (8.00%) aligned >1 times 758s 7.77% overall alignment rate 758s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 758s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 758s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 758s Flattened IUPAC characters 758s Mutating sequence Sim.pm.2 758s Introducing 19 SNPs, 1/0 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutating sequence Sim.pm.1 758s Introducing 1 SNPs, 1/2 ref/read gaps, and 2 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutated reference genome to subject genome 758s SNPs introduced: 20 758s Reference gaps introduced: 2 758s Read gaps introduced: 2 758s Rearrangements introduced: 2 758s Created read sampler 758s Sampling 111 reads 758s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 758s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 758s parsing sequence Sim.pm.1... 758s parsing sequence Sim.pm.2... 758s Parsed 166 reference bases 758s *** Run 94 of 100 758s /usr/bin/bowtie2 --cp-min 2 --np 2 --large-index --mm --score-min L,4.50535352712267,2.86361917732639 -k 3 --local --cp-ival 4 --norc --mp 6.03874153983455,2.18729025261461 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 758s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #2 of read '13' because it was < 2 characters long 758s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '70' because it was < 2 characters long 758s Read 50 alignments... 758s Warning: skipping mate #2 of read '110' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #2 of read '110' because it was < 2 characters long 758s Read 100 alignments... 758s 111 reads; of these: 758s 111 (100.00%) were paired; of these: 758s 111 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 111 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 111 pairs aligned 0 times concordantly or discordantly; of these: 758s 222 mates make up the pairs; of these: 758s 222 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s Read 150 alignments... 758s Read 200 alignments... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s --- Summary --- 758s Read 1 reference strings 758s Checked 0 alignments, 0 edits 758s /usr/bin/bowtie2 --cp-min 2 --np 2 --large-index --mm --score-min L,4.50535352712267,2.86361917732639 -k 3 --local --cp-ival 4 --norc --mp 6.03874153983455,2.18729025261461 -q -p 2 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 758s --------------- 758s PASSED 758s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 758s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #2 of read '13' because it was < 2 characters long 758s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '70' because it was < 2 characters long 758s Warning: skipping mate #2 of read '110' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #2 of read '110' because it was < 2 characters long 758s 111 reads; of these: 758s 111 (100.00diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 758s %) were paired; of these: 758s 111 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 111 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 111 pairs aligned 0 times concordantly or discordantly; of these: 758s 222 mates make up the pairs; of these: 758s 222 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s Flattened IUPAC characters 758s Mutating sequence Sim.pm.1 758s Introducing 5 SNPs, 0/1 ref/read gaps, and 1 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutating sequence Sim.pm.2 758s Introducing 7 SNPs, 2/1 ref/read gaps, and 0 rearrangements 758s *** Run 95 of 100 758s /usr/bin/bowtie2 --cp-ival 3 --cp-min 2 --large-index -a --trim5 3 --norc --mm --score-min L,3.91668039090831,3.6428604049809 --mp 9.97312192186497,5.80455290357908 -q -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fastq -2 /tmp/Sim.pm.pBDT5Pxz_2.fastq 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutated reference genome to subject genome 758s SNPs introduced: 12 758s Reference gaps introduced: 2 758s Read gaps introduced: 2 758s Rearrangements introduced: 1 758s Created read sampler 758s Sampling 78 reads 758s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fastq & /tmp/Sim.pm.pBDT5Pxz_2.fastq 758s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 758s parsing sequence Sim.pm.1... 758s parsing sequence Sim.pm.2... 758s Parsed 166 reference bases 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 758s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '4' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 758s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '9' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 758s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '12' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 758s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '19' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 758s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '22' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 758s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '25' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 758s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '29' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 758s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '45' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 758s Read 50 alignments... 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 758s Warning: skipping mate #1 of read '58' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '58' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 758s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '63' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 758s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '65' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 758s Read 100 alignments... 758s 78 reads; of these: 758s 69 (88.46%) were paired; of these: 758s 69 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 69 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 69 pairs aligned 0 times concordantly or discordantly; of these: 758s 138 mates make up the pairs; of these: 758s 125 (90.58%) aligned 0 times 758s 1 (0.72%) aligned exactly 1 time 758s 12 (8.70%) aligned >1 times 758s 9 (11.54%) were unpaired; of these: 758s 8 (88.89%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 1 (11.11%) aligned >1 times 758s 9.52% overall alignment rate 758s Read 150 alignments... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GCGGTTGCTTT 758s GCGGTTGCTTT 758s Processing line... 758s GCGGTTGCTTT 758s GCGGTTGCTTT 758s Processing line... 758s GCGGTTGCTTT 758s GCGGTTGCTTT 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GGAGGGAT 758s GGAGGGAT 758s Processing line... 758s GGAGGGAT 758s GGAGGGAT 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TAGGAGGGATGGGCC 758s TAGGAGGGATGGGCC 758s Processing line... 758s TAGGAGGGATGGGCC 758s TAGGAGGGATGGGCC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GGGGC 758s GGGGC 758s Processing line... 758s GGGGC 758s GGGGC 758s Processing line... 758s GGGGC 758s GGGGC 758s Processing line... 758s TTCGG 758s TTCGG 758s Processing line... 758s TTCGG 758s TTCGG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TC 758s TC 758s Processing line... 758s TC 758s TC 758s Processing line... 758s TC 758s TC 758s Processing line... 758s TC 758s TC 758s Processing line... 758s TC 758s TC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CGGGGCGGC 758s CGGGGCGGC 758s Processing line... 758s CGGGGCGGC 758s CGGGGCGGC 758s Processing line... 758s CGGGGCGGC 758s CGGGGCGGC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GA 758s GA 758s Processing line... 758s GA 758s GA 758s Processing line... 758s GA 758s GA 758s Processing line... 758s GA 758s GA 758s Processing line... 758s GA 758s GA 758s Processing line... 758s GA 758s GA 758s Processing line... 758s GA 758s GA 758s Processing line... 758s GA 758s GA 758s Processing line... 758s GA 758s GA 758s Processing line... 758s GA 758s GA 758s Processing line... 758s GA 758s GA 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GGGATGGGCCGGGGCGGCG 758s GGGATGGGCCGGGGCGGCG 758s Processing line... 758s GGGATGGGCCGGGGCGGCG 758s GGGATGGGCCGGGGCGGCG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CC 758s CC 758s Processing line... 758s CC 758s CC 758s Processing line... 758s CC 758s CC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s GGC 758s GGC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s AGGG 758s AGGG 758s Processing line... 758s AGGG 758s AGGG 758s Processing line... 758s AGGG 758s AGGG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GCGGTTGCTTTAGGAGGG 758s GCGGTTGCTTTAGGAGGG 758s Processing line... 758s GCGGTTGCTTTAGGAGGG 758s GCGGTTGCTTTAGGAGGG 758s Processing line... 758s GCGGTTGCTTTAGGAGGG 758s GCGGTTGCTTTAGGAGGG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CA 758s CA 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s --- Summary --- 758s Read 1 reference strings 758s Checked 56 alignments, 0 edits 758s --------------- 758s PASSED 758s Flattened IUPAC characters 758s Mutating sequence Sim.pm.2 758s Introducing 0 SNPs, 0/2 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutating sequence Sim.pm.1 758s Introducing 0 SNPs, 0/3 ref/read gaps, and 2 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutated reference genome to subject genome 758s SNPs introduced: 0 758s Reference gaps introduced: 0 758s Read gaps introduced: 5 758s Rearrangements introduced: 2 758s Created read sampler 758s Sampling 118 reads 758s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.raw & /tmp/Sim.pm.pBDT5Pxz_2.raw 758s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 758s parsing sequence Sim.pm.1... 758s parsing sequence Sim.pm.2... 758s Parsed 166 reference bases 758s *** Run 96 of 100 758s /usr/bin/bowtie2 --rdg 13.1460932900281,10.5213156637325 --mp 7.9123892162708,7.12155287821404 --score-min L,9.0371852452684,5.16297657035897 --ma 5.89713725273342 --cp-ival 1 -M 5 --large-index --np 1 --cp-min 6 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw 758s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 758s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 758s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 758s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '10' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 758s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '25' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 758s 118 reads; of these: 758s 118 (100.00%) were unpaired; of these: 758s 76 (64.41%) aligned 0 times 758s 8 (6.78%) aligned exactly 1 time 758s 34 (28.81%) aligned >1 times 758s 35.59% overall alignment rate 758s Read 50 alignments... 758s Read 100 alignments... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GCG 758s GCG 758s Processing line... 758s GCG 758s GCG 758s Processing line... 758s GCGGTTGCTTT 758s GCGGTTGCTTT 758s Processing line... 758s GG 758s GG 758s Processing line... 758s Processing line... 758s Processing line... 758s GGAT 758s GGAT 758s Processing line... 758s GTCTGAG 758s GTCTGAG 758s Processing line... 758s Processing line... 758s TG 758s TG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GCGGT 758s GCGGT 758s Processing line... 758s ATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGT 758s ATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGT 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TTG 758s TTG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s ATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTG 758s ATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGGTTG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GTCTG 758s GTCTG 758s Processing line... 758s TGCTTTAGG 758s TGCTTTAGG 758s Processing line... 758s Processing line... 758s TG 758s TG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GGCGG 758s GGCGG 758s Processing line... 758s Processing line... 758s TGGG 758s TGGG 758s Processing line... 758s Processing line... 758s TCATTGTAGTGGC 758s TCATTGTAGTGGC 758s Processing line... 758s TCG 758s TCG 758s Processing line... 758s Processing line... 758s GCTTTAGGAGGGATGGGCCGGGGCGGCGGTTG 758s GCTTTAGGAGGGATGGGCCGGGGCGGCGGTTG 758s Processing line... 758s Processing line... 758s TTGCTTTAGGAGGGATGGGCCG 758s TTGCTTTAGGAGGGATGGGCCG 758s Processing line... 758s CCGGGGC 758s CCGGGGC 758s Processing line... 758s TGGG 758s TGGG 758s Processing line... 758s Processing line... 758s GAG 758s GAG 758s Processing line... 758s TGCTTTAGG 758s TGCTTTAGG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GCTTTAGGAGGGA 758s GCTTTAGGAGGGA 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CC 758s CC 758s Processing line... 758s AGGAGG 758s AGGAGG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TCTG 758s TCTG 758s Processing line... 758s Processing line... 758s GCTTTAGGAGGGATGGGC 758s GCTTTAGGAGGGATGGGC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GCGGTCT 758s GCGGTCT 758s Processing line... 758s Processing line... 758s Processing line... 758s GG 758s GG 758s Processing line... 758s Processing line... 758s TGGGCGGTTGACTTT 758s TGGGCGGTTGACTTT 758s Processing line... 758s Processing line... 758s AGGGATGGGCCGGGGCGGCGGTTGCTTTAG 758s AGGGATGGGCCGGGGCGGCGGTTGCTTTAG 758s Processing line... 758s Processing line... 758s TGATCGGGAGTGGGCGGTTGACTTTCGGCG 758s TGATCGGGAGTGGGCGGTTGACTTTCGGCG 758s Processing line... 758s Processing line... 758s Processing line... 758s GCTTTAGGAGGGA 758s GCTTTAGGAGGGA 758s Processing line... 758s Processing line... 758s GATGGGCCGGGGCGGCG 758s GATGGGCCGGGGCGGCG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GCTTTAGG 758s GCTTTAGG 758s Processing line... 758s CGGTTGCTTTAG 758s CGGTTGCTTTAG 758s Processing line... 758s Processing line... 758s Processing line... 758s TTG 758s TTG 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s GGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGG 758s GGTTGCTTTAGGAGGGATGGGCCGGGGCGGCGG 758s Processing line... 758s CGGCGGTTGCTTTAGGA 758s CGGCGGTTGCTTTAGGA 758s Processing line... 758s TAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGA 758s TAGGAGGGATGGGCCGGGGCGGCGGTTGCTTTAGGA 758s Processing line... 758s --- Summary --- 758s Read 1 reference strings 758s Checked 42 alignments, 0 edits 758s --------------- 758s PASSED 758s ALSO checking that bowtie2 and bowtie2-align match up 758s /usr/bin/bowtie2 --rdg 13.1460932900281,10.5213156637325 --mp 7.9123892162708,7.12155287821404 --score-min L,9.0371852452684,5.16297657035897 --ma 5.89713725273342 --cp-ival 1 -M 5 --large-index --np 1 --cp-min 6 -r -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.raw | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.als 758s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 758s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 758s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 758s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '10' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 758s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '25' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 758s 118 reads; of these: 758s 118 (100.00%) were unpaired; of these: 758s 76 (64.41%) aligned 0 times 758s 8 (6.78%) aligned exactly 1 time 758s 34 (28.81%) aligned >1 times 758s 35.59% overall alignment rate 758s diff -uw /tmp/Sim.pm.pBDT5Pxz.als /tmp/Sim.pm.pBDT5Pxz.debug.als 758s Flattened IUPAC characters 758s Mutating sequence Sim.pm.1 758s Introducing 11 SNPs, 1/2 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutating sequence Sim.pm.2 758s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutated reference genome to subject genome 758s SNPs introduced: 13 758s Reference gaps introduced: 1 758s Read gaps introduced: 3 758s Rearrangements introduced: 1 758s Created read sampler 758s Sampling 28 reads 758s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 758s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 758s parsing sequence Sim.pm.1... 758s parsing sequence Sim.pm.2... 758s Parsed 166 reference bases 758s *** Run 97 of 100 758s /usr/bin/bowtie2 --rfg 47.6863905793723,5.62677533099237 --trim3 6 --mp 8.76590243638573,7.56330639630605 --local --cp-ival 2 --norc --rdg 16.7232767396972,9.04931797654928 --mm --score-min L,1.75139841338101,3.08503624434959 -D 4 --large-index --cp-min 4 --np 3 -f -x /tmp/Sim.pm.pBDT5Pxz -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta 758s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '20' because it was < 2 characters long 758s 28 reads; of these: 758s 26 (92.86%) were paired; of these: 758s 26 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 26 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 26 pairs aligned 0 times concordantly or discordantly; of these: 758s 52 mates make up the pairs; of these: 758s 52 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 2 (7.14%) were unpaired; of these: 758s 2 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s Read 50 alignments... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s /usr/bin/bowtie2 --rfg 47.6863905793723,5.62677533099237 --trim3 6 --mp 8.76590243638573,7.56330639630605 --local --cp-ival 2 --norc --rdg 16.7232767396972,9.04931797654928 --mm --score-min L,1.75139841338101,3.08503624434959 -D 4 --large-index --cp-min 4 --np 3 -f -p 3 -x /tmp/Sim.pm.pBDT5Pxz --reorder -1 /tmp/Sim.pm.pBDT5Pxz_1.fasta -2 /tmp/Sim.pm.pBDT5Pxz_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.reord.als 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s --- Summary --- 758s Read 1 reference strings 758s Checked 0 alignments, 0 edits 758s --------------- 758s PASSED 758s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 758s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '20' because it was < 2 characters long 758s 28 reads; of these: 758s 26 (92.86%) were paired; of these: 758s 26 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 26 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 26 pairs aligned 0 times concordantly or discordantly; of these: 758s 52 mates make up the pairs; of these: 758s 52 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 2 (7.14%) were unpaired; of these: 758s 2 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als /tmp/Sim.pm.pBDT5Pxz.px.reord.als 758s Flattened IUPAC characters 758s Mutating sequence Sim.pm.2 758s Introducing 22 SNPs, 0/2 ref/read gaps, and 1 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutating sequence Sim.pm.1 758s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 758s *** Run 98 of 100 758s /usr/bin/bowtie2 --trim5 7 --large-index --cp-min 4 --cp-ival 1 --local -k 2 -D 16 -R 2 --score-min L,4.59077083189763,3.25883088540315 --trim3 2 --rfg 48.1995394374062,15.8362946119555 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutated reference genome to subject genome 758s SNPs introduced: 22 758s Reference gaps introduced: 1 758s Read gaps introduced: 2 758s Rearrangements introduced: 1 758s Created read sampler 758s Sampling 26 reads 758s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 758s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 758s parsing sequence Sim.pm.1... 758s parsing sequence Sim.pm.2... 758s Parsed 166 reference bases 758s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '1' because it was < 2 characters long 758s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '2' because it was < 2 characters long 758s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '5' because it was < 2 characters long 758s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '6' because it was < 2 characters long 758s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '8' because it was < 2 characters long 758s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '10' because it was < 2 characters long 758s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '14' because it was < 2 characters long 758s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '25' because it was < 2 characters long 759s 26 reads; of these: 759s 26 (100.00%) were unpaired; of these: 759s 26 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 0.00% overall alignment rate 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s /usr/bin/bowtie2 --trim5 7 --large-index --cp-min 4 --cp-ival 1 --local -k 2 -D 16 -R 2 --score-min L,4.59077083189763,3.25883088540315 --trim3 2 --rfg 48.1995394374062,15.8362946119555 -f -p 2 -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s --- Summary --- 759s Read 1 reference strings 759s Checked 0 alignments, 0 edits 759s --------------- 759s PASSED 759s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 759s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '1' because it was < 2 characters long 759s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '2' because it was < 2 characters long 759s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '5' because it was < 2 characters long 759s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '6' because it was < 2 characters long 759s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '8' because it was < 2 characters long 759s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '10' because it was < 2 characters long 759s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '14' because it was < 2 characters long 759s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '25' because it was < 2 characters long 759s 26 reads; of these: 759s 26 (100.00%) were unpaired; of these: 759s 26 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 0.00% overall alignment rate 759s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.px.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 759s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.pBDT5Pxz.debug.als | grep -v '^@PG' > /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted 759s diff -uw /tmp/Sim.pm.pBDT5Pxz.debug.als.sorted /tmp/Sim.pm.pBDT5Pxz.px.als.sorted 759s Flattened IUPAC characters 759s Mutating sequence Sim.pm.1 759s Introducing 7 SNPs, 0/1 ref/read gaps, and 1 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutating sequence Sim.pm.2 759s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutated reference genome to subject genome 759s SNPs introduced: 13 759s Reference gaps introduced: 1 759s Read gaps introduced: 1 759s Rearrangements introduced: 1 759s Created read sampler 759s Sampling 105 reads 759s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.fasta & /tmp/Sim.pm.pBDT5Pxz_2.fasta 759s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 759s parsing sequence Sim.pm.1... 759s parsing sequence Sim.pm.2... 759s Parsed 166 reference bases 759s *** Run 99 of 100 759s /usr/bin/bowtie2 --cp-ival 2 --large-index --cp-min 6 --np 1 --trim5 3 --norc --score-min L,7.33504164101488,5.2147622794168 --gbar 1 -f -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.fasta 759s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 759s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '11' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 759s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '24' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 759s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '26' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 759s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '28' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 759s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '34' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 759s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '42' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 759s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '49' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 759s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '56' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 759s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '62' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 759s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '69' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 759s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '87' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 759s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '88' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 759s 105 reads; of these: 759s 105 (100.00%) were unpaired; of these: 759s 90 (85.71%) aligned 0 times 759s 5 (4.76%) aligned exactly 1 time 759s 10 (9.52%) aligned >1 times 759s 14.29% overall alignment rate 759s Read 50 alignments... 759s Read 100 alignments... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s CGGT 759s CGGT 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GG 759s GG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s CATTG 759s CATTG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GC 759s GC 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGC 759s GATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGATGGGC 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s TC 759s TC 759s Processing line... 759s Processing line... 759s GGTG 759s GGTG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GGGCCGGGGCGGCGG 759s GGGCCGGGGCGGCGG 759s Processing line... 759s TAGGAGGGATGGGCCGGG 759s TAGGAGGGATGGGCCGGG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGA 759s GGATGGGCCGGGGCGGCGGTTGCTTTAGGAGGGA 759s Processing line... 759s GGGCGGTTGACTTTCGG 759s GGGCGGTTGACTTTCGG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s CTTTCGGGTGTCATTGTAGT 759s CTTTCGGGTGTCATTGTAGT 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s CCG 759s CCG 759s Processing line... 759s Processing line... 759s Processing line... 759s GGGCGGCGGTTGCTTTA 759s GGGCGGCGGTTGCTTTA 759s Processing line... 759s Processing line... 759s CC 759s CC 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s --- Summary --- 759s Read 1 reference strings 759s Checked 15 alignments, 0 edits 759s --------------- 759s PASSED 759s Flattened IUPAC characters 759s Mutating sequence Sim.pm.2 759s Introducing 13 SNPs, 1/2 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutating sequence Sim.pm.1 759s Introducing 7 SNPs, 1/0 ref/read gaps, and 1 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutated reference genome to subject genome 759s SNPs introduced: 20 759s Reference gaps introduced: 2 759s Read gaps introduced: 2 759s Rearrangements introduced: 1 759s Created read sampler 759s Sampling 113 reads 759s Dumping reads to temporary files /tmp/Sim.pm.pBDT5Pxz_1.qseq & /tmp/Sim.pm.pBDT5Pxz_2.qseq 759s Parsing FASTA file /tmp/Sim.pm.pBDT5Pxz.fa... 759s parsing sequence Sim.pm.1... 759s *** Run 100 of 100 759s /usr/bin/bowtie2 --rfg 19.531218828705,6.92605472435926 --rdg 44.8839434460435 --gbar 1 --mp 6.25654819412464,3.06115317121056 -N 1 -L30 --score-min L,5.94289231074315,1.0263567866014 --cp-ival 2 --large-index --cp-min 8 --np 1 --qseq -x /tmp/Sim.pm.pBDT5Pxz /tmp/Sim.pm.pBDT5Pxz_1.qseq 759s parsing sequence Sim.pm.2... 759s Parsed 166 reference bases 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (1) 759s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (1) <= # seed mismatches (1) 759s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (1) 759s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (1) <= # seed mismatches (1) 759s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (1) <= # seed mismatches (1) 759s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 759s Read 50 alignments... 759s 113 reads; of these: 759s 113 (100.00%) were unpaired; of these: 759s 92 (81.42%) aligned 0 times 759s 4 (3.54%) aligned exactly 1 time 759s 17 (15.04%) aligned >1 times 759s 18.58% overall alignment rate 759s Read 100 alignments... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GTGGCG 759s GTGGCG 759s Processing line... 759s Processing line... 759s Processing line... 759s GCGGCGGTTGCT 759s GCGGCGGTTGCT 759s Processing line... 759s Processing line... 759s CG 759s CG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GGGCCGGGGCGGCGGTTGCTTT 759s GGGCCGGGGCGGCGGTTGCTTT 759s Processing line... 759s GGATGGGCCGGGGCGG 759s GGATGGGCCGGGGCGG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s AGTGGGCG 759s AGTGGGCG 759s Processing line... 759s CGG 759s CGG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s TT 759s TT 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s CCGGGGCGGCGGTTGCTTTAGGAGG 759s CCGGGGCGGCGGTTGCTTTAGGAGG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GTTGCTT 759s GTTGCTT 759s Processing line... 759s Processing line... 759s CTTTAGG 759s CTTTAGG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s AGTGGGCG 759s AGTGGGCG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GGCGG 759s GGCGG 759s Processing line... 759s Processing line... 759s GGG 759s GGG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GGA 759s GGA 759s Processing line... 759s Processing line... 759s ATGGGC 759s ATGGGC 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s TTC 759s TTC 759s Processing line... 759s Processing line... 759s Processing line... 759s GGCC 759s GGCC 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GCCG 759s GCCG 759s Processing line... 759s GGA 759s GGA 759s Processing line... 759s CGGTTGACTTTCGGGTGTCA 759s CGGTTGACTTTCGGGTGTCA 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s --- Summary --- 759s Read 1 reference strings 759s Checked 21 alignments, 0 edits 759s --------------- 759s PASSED 759s Created DNA generator 759s N frac: 0.009 759s IUPAC frac: 0.010 759s AT/ACGT frac: 0.328 759s A/AT frac: 0.269 759s C/CG frac: 0.283 759s Generating 2 references 759s Generated reference 'Sim.pm.1' of untrimmed length 297, trimmed length 5 759s Generated reference 'Sim.pm.2' of untrimmed length 311, trimmed length 71 759s Wrote references to /tmp/Sim.pm.qJbFQMAC.fa 759s A: 5 759s C: 11 759s G: 39 759s N: 2 759s T: 19 759s Executing: /usr/bin/bowtie2-build --bmax 34026 --threads 1 --dcv 4096 --large-index /tmp/Sim.pm.qJbFQMAC.fa /tmp/Sim.pm.qJbFQMAC 759s *** TEST CASE *** 759s Settings: 759s Output files: "/tmp/Sim.pm.qJbFQMAC.*.bt2l" 759s Line rate: 7 (line is 128 bytes) 759s Lines per side: 1 (side is 128 bytes) 759s Offset rate: 4 (one in 16) 759s FTable chars: 10 759s Strings: unpacked 759s Max bucket size: 34026 759s Max bucket size, sqrt multiplier: default 759s Max bucket size, len divisor: default 759s Difference-cover sample period: 4096 759s Endianness: little 759s Actual local endianness: little 759s Sanity checking: disabled 759s Assertions: disabled 759s Random seed: 0 759s Sizeofs: void*:8, int:4, long:8, size_t:8 759s Input files DNA, FASTA: 759s /tmp/Sim.pm.qJbFQMAC.fa 759s Reading reference sizes 759s Time reading reference sizes: 00:00:00 759s Calculating joined length 759s Writing header 759s Reserving space for joined string 759s Joining reference sequences 759s Time to join reference sequences: 00:00:00 759s bmax according to bmax setting: 34026 759s Using parameters --bmax 25520 --dcv 4096 759s Doing ahead-of-time memory usage test 759s Building a LARGE index 759s Passed! Constructing with these parameters: --bmax 25520 --dcv 4096 759s Constructing suffix-array element generator 759s Building DifferenceCoverSample 759s Building sPrime 759s Building sPrimeOrder 759s V-Sorting samples 759s V-Sorting samples time: 00:00:00 759s Allocating rank array 759s Ranking v-sort output 759s Ranking v-sort output time: 00:00:00 759s Invoking Larsson-Sadakane on ranks 759s Invoking Larsson-Sadakane on ranks time: 00:00:00 759s Sanity-checking and returning 759s Skipping building samples since text length 74 is less than bucket size: 25520 759s Converting suffix-array elements to index image 759s Allocating ftab, absorbFtab 759s Entering Ebwt loop 759s Getting block 1 of 1 759s No samples; assembling all-inclusive block 759s Sorting block of length 74 for bucket 1 759s (Using difference cover) 759s Sorting block time: 00:00:00 759s Returning block of 75 for bucket 1 759s Exited Ebwt loop 759s fchr[A]: 0 759s fchr[C]: 5 759s fchr[G]: 16 759s fchr[T]: 55 759s fchr[$]: 74 759s Exiting Ebwt::buildToDisk() 759s Returning from initFromVector 759s Wrote 8389131 bytes to primary EBWT file: /tmp/Sim.pm.qJbFQMAC.1.bt2l.tmp 759s Wrote 44 bytes to secondary EBWT file: /tmp/Sim.pm.qJbFQMAC.2.bt2l.tmp 759s Re-opening _in1 and _in2 as input streams 759s Returning from Ebwt constructor 759s Headers: 759s len: 74 759s bwtLen: 75 759s sz: 19 759s bwtSz: 19 759s lineRate: 7 759s offRate: 4 759s offMask: 0xfffffffffffffff0 759s ftabChars: 10 759s eftabLen: 20 759s eftabSz: 160 759s ftabLen: 1048577 759s ftabSz: 8388616 759s offsLen: 5 759s offsSz: 40 759s lineSz: 128 759s sideSz: 128 759s sideBwtSz: 96 759s sideBwtLen: 384 759s numSides: 1 759s numLines: 1 759s ebwtTotLen: 128 759s ebwtTotSz: 128 759s color: 0 759s reverse: 0 759s Total time for call to driver() for forward index: 00:00:00 759s Reading reference sizes 759s Time reading reference sizes: 00:00:00 759s Calculating joined length 759s Writing header 759s Reserving space for joined string 759s Joining reference sequences 759s Time to join reference sequences: 00:00:00 759s Time to reverse reference sequence: 00:00:00 759s bmax according to bmax setting: 34026 759s Using parameters --bmax 25520 --dcv 4096 759s Doing ahead-of-time memory usage test 759s Passed! Constructing with these parameters: --bmax 25520 --dcv 4096 759s Constructing suffix-array element generator 759s Building DifferenceCoverSample 759s Building sPrime 759s Building sPrimeOrder 759s V-Sorting samples 759s V-Sorting samples time: 00:00:00 759s Allocating rank array 759s Ranking v-sort output 759s Ranking v-sort output time: 00:00:00 759s Invoking Larsson-Sadakane on ranks 759s Invoking Larsson-Sadakane on ranks time: 00:00:00 759s Sanity-checking and returning 759s Skipping building samples since text length 74 is less than bucket size: 25520 759s Converting suffix-array elements to index image 759s Allocating ftab, absorbFtab 759s Entering Ebwt loop 759s Getting block 1 of 1 759s No samples; assembling all-inclusive block 759s Sorting block of length 74 for bucket 1 759s (Using difference cover) 759s Sorting block time: 00:00:00 759s Returning block of 75 for bucket 1 759s Exited Ebwt loop 759s fchr[A]: 0 759s fchr[C]: 5 759s fchr[G]: 16 759s fchr[T]: 55 759s fchr[$]: 74 759s Exiting Ebwt::buildToDisk() 759s Returning from initFromVector 759s Wrote 8389131 bytes to primary EBWT file: /tmp/Sim.pm.qJbFQMAC.rev.1.bt2l.tmp 759s Wrote 44 bytes to secondary EBWT file: /tmp/Sim.pm.qJbFQMAC.rev.2.bt2l.tmp 759s Re-opening _in1 and _in2 as input streams 759s Returning from Ebwt constructor 759s Headers: 759s len: 74 759s bwtLen: 75 759s sz: 19 759s bwtSz: 19 759s lineRate: 7 759s offRate: 4 759s offMask: 0xfffffffffffffff0 759s ftabChars: 10 759s eftabLen: 20 759s eftabSz: 160 759s ftabLen: 1048577 759s ftabSz: 8388616 759s offsLen: 5 759s offsSz: 40 759s lineSz: 128 759s sideSz: 128 759s sideBwtSz: 96 759s sideBwtLen: 384 759s numSides: 1 759s numLines: 1 759s ebwtTotLen: 128 759s ebwtTotSz: 128 759s color: 0 759s reverse: 1 759s Total time for backward call to driver() for mirror index: 00:00:00 759s Renaming /tmp/Sim.pm.qJbFQMAC.3.bt2l.tmp to /tmp/Sim.pm.qJbFQMAC.3.bt2l 759s Renaming /tmp/Sim.pm.qJbFQMAC.4.bt2l.tmp to /tmp/Sim.pm.qJbFQMAC.4.bt2l 759s Renaming /tmp/Sim.pm.qJbFQMAC.1.bt2l.tmp to /tmp/Sim.pm.qJbFQMAC.1.bt2l 759s Renaming /tmp/Sim.pm.qJbFQMAC.2.bt2l.tmp to /tmp/Sim.pm.qJbFQMAC.2.bt2l 759s Renaming /tmp/Sim.pm.qJbFQMAC.rev.1.bt2l.tmp to /tmp/Sim.pm.qJbFQMAC.rev.1.bt2l 759s Renaming /tmp/Sim.pm.qJbFQMAC.rev.2.bt2l.tmp to /tmp/Sim.pm.qJbFQMAC.rev.2.bt2l 759s Built nucleotide index '/tmp/Sim.pm.qJbFQMAC' 759s Flattened IUPAC characters 759s Mutating sequence Sim.pm.2 759s *** Run 1 of 100 759s /usr/bin/bowtie2 --cp-ival 1 --large-index -M 3 --cp-min 7 --trim5 6 --rdg 45.6409016277067,4.63283043344998 --score-min L,1.58181880947882,3.25410073418103 --nofw --ma 12.7572986229185 -D 8 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 759s Introducing 14 SNPs, 0/1 ref/read gaps, and 1 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutating sequence Sim.pm.1 759s Introducing 14 SNPs, 4/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutated reference genome to subject genome 759s SNPs introduced: 28 759s Reference gaps introduced: 4 759s Read gaps introduced: 1 759s Rearrangements introduced: 1 759s Created read sampler 759s Sampling 102 reads 759s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 759s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 759s parsing sequence Sim.pm.1... 759s parsing sequence Sim.pm.2... 759s Parsed 76 reference bases 759s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 759s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 759s Read 50 alignments... 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 759s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 759s 102 reads; of these: 759s 86 (84.31%) were paired; of these: 759s 86 (100.00%) aligned concordantly 0 times 759s 0 (0.00%) aligned concordantly exactly 1 time 759s 0 (0.00%) aligned concordantly >1 times 759s ---- 759s 86 pairs aligned concordantly 0 times; of these: 759s 0 (0.00%) aligned discordantly 1 time 759s ---- 759s 86 pairs aligned 0 times concordantly or discordantly; of these: 759s 172 mates make up the pairs; of these: 759s 160 (93.02%) aligned 0 times 759s 6 (3.49%) aligned exactly 1 time 759s 6 (3.49%) aligned >1 times 759s 16 (15.69%) were unpaired; of these: 759s 16 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 6.38% overall alignment rate 759s Read 100 alignments... 759s Read 150 alignments... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GG 759s GG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s TCGGTTCGGGGGTGGCTGGGG 759s TCGGTTCGGGGGTGGCTGGGG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GGGGT 759s GGGGT 759s Processing line... 759s Processing line... 759s GAGTTC 759s GAGTTC 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s TCGGGGGTGG 759s TCGGGGGTGG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s TCGGTTCGGGGGT 759s TCGGTTCGGGGGT 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s CG 759s CG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s AGT 759s AGT 759s Processing line... 759s Processing line... 759s GGCGATT 759s GGCGATT 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s TGGG 759s TGGG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GA 759s GA 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s CC 759s CC 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s --- Summary --- 759s Read 1 reference strings 759s Checked 12 alignments, 0 edits 759s --------------- 759s PASSED 759s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 759s /usr/bin/bowtie2 --cp-ival 1 --large-index -M 3 --cp-min 7 --trim5 6 --rdg 45.6409016277067,4.63283043344998 --score-min L,1.58181880947882,3.25410073418103 --nofw --ma 12.7572986229185 -D 8 --qseq -p 2 -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 759s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 759s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 760s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 760s 102 reads; of these: 760s 86 (84.31%) were paired; of these: 760s 86 (100.00%) aligned concordantly 0 times 760s 0 (0.00%) aligned concordantly exactly 1 time 760s 0 (0.00%) aligned concordantly >1 times 760s ---- 760s 86 pairs aligned concordantly 0 times; of these: 760s 0 (0.00%) aligned discordantly 1 time 760s ---- 760s 86 pairs aligned 0 times concordantly or discordantly; of these: 760s 172 mates make up the pairs; of these: 760s 160 (93.02%) aligned 0 times 760s 6 (3.49%) aligned exactly 1 time 760s 6 (3.49%) aligned >1 times 760s 16 (15.69%) were unpaired; of these: 760s 16 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 6.38% overall alignment rate 760s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 760s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 760s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 760s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 760s /usr/bin/bowtie2 --cp-ival 1 --large-index -M 3 --cp-min 7 --trim5 6 --rdg 45.6409016277067,4.63283043344998 --score-min L,1.58181880947882,3.25410073418103 --nofw --ma 12.7572986229185 -D 8 --qseq -p 2 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 760s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 760s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 760s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 760s 102 reads; of these: 760s 86 (84.31%) were paired; of these: 760s 86 (100.00%) aligned concordantly 0 times 760s 0 (0.00%) aligned concordantly exactly 1 time 760s 0 (0.00%) aligned concordantly >1 times 760s ---- 760s 86 pairs aligned concordantly 0 times; of these: 760s 0 (0.00%) aligned discordantly 1 time 760s ---- 760s 86 pairs aligned 0 times concordantly or discordantly; of these: 760s 172 mates make up the pairs; of these: 760s 160 (93.02%) aligned 0 times 760s 6 (3.49%) aligned exactly 1 time 760s 6 (3.49%) aligned >1 times 760s 16 (15.69%) were unpaired; of these: 760s 16 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 6.38% overall alignment rate 760s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.2 760s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutating sequence Sim.pm.1 760s Introducing 10 SNPs, 1/0 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 14 760s Reference gaps introduced: 1 760s Read gaps introduced: 0 760s Rearrangements introduced: 0 760s Created read sampler 760s Sampling 138 reads 760s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 760s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 760s parsing sequence Sim.pm.1... 760s parsing sequence Sim.pm.2... 760s Parsed 76 reference bases 760s *** Run 2 of 100 760s /usr/bin/bowtie2 --cp-min 2 --np 4 --large-index --rdg 33.85991605329,10.5435635113171 -D 6 --score-min L,4.08884083319058,9.63342266801788 --cp-ival 1 --local --n-ceil 0.0364755623044552,0.843470508789175 --trim5 5 --norc -M 4 --rfg 30.6141980649935 --mp 9.85235045219296,3.47436735142079 --trim3 8 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 760s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 760s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '1' because it was < 2 characters long 760s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '8' because it was < 2 characters long 760s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '14' because it was < 2 characters long 760s Warning: skipping mate #2 of read '14' because it was < 2 characters long 760s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '15' because it was < 2 characters long 760s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '19' because it was < 2 characters long 760s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '20' because it was < 2 characters long 760s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read '21' because it was < 2 characters long 760s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '23' because it was < 2 characters long 760s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '27' because it was < 2 characters long 760s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '30' because it was < 2 characters long 760s Warning: skipping mate #1 of read '34' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '34' because it was < 2 characters long 760s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '35' because it was < 2 characters long 760s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '37' because it was < 2 characters long 760s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '42' because it was < 2 characters long 760s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '45' because it was < 2 characters long 760s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '48' because it was < 2 characters long 760s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '49' because it was < 2 characters long 760s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '53' because it was < 2 characters long 760s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '54' because it was < 2 characters long 760s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '55' because it was < 2 characters long 760s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '56' because it was < 2 characters long 760s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '57' because it was < 2 characters long 760s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '58' because it was < 2 characters long 760s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '65' because it was < 2 characters long 760s Read 50 alignments... 760s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '66' because it was < 2 characters long 760s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '77' because it was < 2 characters long 760s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '78' because it was < 2 characters long 760s Warning: skipping mate #2 of read '79' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read '79' because it was < 2 characters long 760s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '82' because it was < 2 characters long 760s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '86' because it was < 2 characters long 760s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '87' because it was < 2 characters long 760s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '90' because it was < 2 characters long 760s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '92' because it was < 2 characters long 760s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '96' because it was < 2 characters long 760s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '98' because it was < 2 characters long 760s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read '100' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '100' because it was < 2 characters long 760s Warning: skipping mate #2 of read '100' because it was < 2 characters long 760s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '103' because it was < 2 characters long 760s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '110' because it was < 2 characters long 760s Warning: skipping mate #1 of read '111' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '111' because it was < 2 characters long 760s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '115' because it was < 2 characters long 760s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '116' because it was < 2 characters long 760s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '119' because it was < 2 characters long 760s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '123' because it was < 2 characters long 760s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '124' because it was < 2 characters long 760s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '129' because it was < 2 characters long 760s Warning: skipping mate #2 of read '131' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read '131' because it was < 2 characters long 760s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '136' because it was < 2 characters long 760s Read 100 alignments... 760s Read 150 alignments... 760s 138 reads; of these: 760s 104 (75.36%) were paired; of these: 760s 104 (100.00%) aligned concordantly 0 times 760s 0 (0.00%) aligned concordantly exactly 1 time 760s 0 (0.00%) aligned concordantly >1 times 760s ---- 760s Read 200 alignments... 760s 104 pairs aligned concordantly 0 times; of these: 760s 0 (0.00%) aligned discordantly 1 time 760s ---- 760s 104 pairs aligned 0 times concordantly or discordantly; of these: 760s 208 mates make up the pairs; of these: 760s 208 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 34 (24.64%) were unpaired; of these: 760s 34 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 0.00% overall alignment rate 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s /usr/bin/bowtie2 --cp-min 2 --np 4 --large-index --rdg 33.85991605329,10.5435635113171 -D 6 --score-min L,4.08884083319058,9.63342266801788 --cp-ival 1 --local --n-ceil 0.0364755623044552,0.843470508789175 --trim5 5 --norc -M 4 --rfg 30.6141980649935 --mp 9.85235045219296,3.47436735142079 --trim3 8 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing 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Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s --- Summary --- 760s Read 1 reference strings 760s Checked 0 alignments, 0 edits 760s --------------- 760s PASSED 760s ALSO checking that bowtie2 and bowtie2-align match up 760s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 760s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '1' because it was < 2 characters long 760s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '8' because it was < 2 characters long 760s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '14' because it was < 2 characters long 760s Warning: skipping mate #2 of read '14' because it was < 2 characters long 760s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '15' because it was < 2 characters long 760s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '19' because it was < 2 characters long 760s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '20' because it was < 2 characters long 760s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read '21' because it was < 2 characters long 760s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '23' because it was < 2 characters long 760s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '27' because it was < 2 characters long 760s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '30' because it was < 2 characters long 760s Warning: skipping mate #1 of read '34' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '34' because it was < 2 characters long 760s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '35' because it was < 2 characters long 760s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '37' because it was < 2 characters long 760s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '42' because it was < 2 characters long 760s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '45' because it was < 2 characters long 760s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '48' because it was < 2 characters long 760s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '49' because it was < 2 characters long 760s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '53' because it was < 2 characters long 760s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '54' because it was < 2 characters long 760s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '55' because it was < 2 characters long 760s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '56' because it was < 2 characters long 760s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '57' because it was < 2 characters long 760s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '58' because it was < 2 characters long 760s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '65' because it was < 2 characters long 760s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '66' because it was < 2 characters long 760s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '77' because it was < 2 characters long 760s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '78' because it was < 2 characters long 760s Warning: skipping mate #2 of read '79' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read '79' because it was < 2 characters long 760s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '82' because it was < 2 characters long 760s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '86' because it was < 2 characters long 760s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '87' because it was < 2 characters long 760s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '90' because it was < 2 characters long 760s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '92' because it was < 2 characters long 760s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '96' because it was < 2 characters long 760s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '98' because it was < 2 characters long 760s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read '100' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '100' because it was < 2 characters long 760s Warning: skipping mate #2 of read '100' because it was < 2 characters long 760s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '103' because it was < 2 characters long 760s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '110' because it was < 2 characters long 760s Warning: skipping mate #1 of read '111' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '111' because it was < 2 characters long 760s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '115' because it was < 2 characters long 760s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '116' because it was < 2 characters long 760s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '119' because it was < 2 characters long 760s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '123' because it was < 2 characters long 760s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '124' because it was < 2 characters long 760s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '129' because it was < 2 characters long 760s Warning: skipping mate #2 of read '131' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read '131' because it was < 2 characters long 760s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '136' because it was < 2 characters long 760s 138 reads; of these: 760s 104 (75.36%) were paired; of these: 760s 104 (100.00%) aligned concordantly 0 times 760s 0 (0.00%) aligned concordantly exactly 1 time 760s 0 (0.00%) aligned concordantly >1 times 760s ---- 760s 104 pairs aligned concordantly 0 times; of these: 760s 0 (0.00%) aligned discordantly 1 time 760s ---- 760s 104 pairs aligned 0 times concordantly or discordantly; of these: 760s 208 mates make up the pairs; of these: 760s 208 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 34 (24.64%) were unpaired; of these: 760s 34 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 0.00% overall alignment rate 760s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.2 760s Introducing 4 SNPs, 1/1 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutating sequence Sim.pm.1 760s Introducing 2 SNPs, 2/0 ref/read gaps, and 1 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 6 760s Reference gaps introduced: 3 760s Read gaps introduced: 1 760s Rearrangements introduced: 1 760s Created read sampler 760s Sampling 93 reads 760s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 760s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 760s parsing sequence Sim.pm.1... 760s *** Run 3 of 100 760s /usr/bin/bowtie2 --score-min L,8.93633593413446,1.15396800687876 --mp 9.64031406791261,4.4765457420174 -N 1 -L30 --gbar 5 --rdg 45.2209068521751,16.5735535080321 --cp-min 10 --large-index --local --cp-ival 1 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 760s parsing sequence Sim.pm.2... 760s Parsed 76 reference bases 760s Warning: skipping read '37' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '37' because it was < 2 characters long 760s Warning: skipping read '41' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '41' because it was < 2 characters long 760s Warning: skipping read '64' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '64' because it was < 2 characters long 760s Warning: skipping read '66' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '66' because it was < 2 characters long 760s Warning: skipping read '93' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '93' because it was < 2 characters long 760s 93 reads; of these: 760s 93 (100.00%) were unpaired; of these: 760s 84 (90.32%) aligned 0 times 760s 9 (9.68%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 9.68% overall alignment rate 760s Read 50 alignments... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GCTCTCGGTTCGGGGGTGGCTGGGG 760s GCTCTCGGTTCGGGGGTGGCTGGGG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s ACCTGGGGGTTGCTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGTTGGAG 760s ACCTGGGGGNTGCTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGTTG--G 760s Processing line... 760s Processing line... 760s Processing line... 760s /usr/bin/bowtie2 --score-min L,8.93633593413446,1.15396800687876 --mp 9.64031406791261,4.4765457420174 -N 1 -L30 --gbar 5 --rdg 45.2209068521751,16.5735535080321 --cp-min 10 --large-index --local --cp-ival 1 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s TCGGTTCGGGGGTGGCTGGGGGGTA 760s TCGGTTCGGGGGTGGCTGGGGGGTA 760s Processing line... 760s TCGGGGGTGGCTGGGGGG 760s TCGGGGGTGGCTGGGGGG 760s Processing line... 760s GGTGGCTGGGG 760s GGTGGCTGGGG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CGGGGGTGGCT 760s CGGGGGTGGCT 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GGGGCGATTAG 760s GGGGCGATTAG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GATGCTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGTT 760s GNTGCTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAG-T 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGTTGGGGTTCTGG 760s GGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGTTGGAGTTCTGG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s --- Summary --- 760s Read 1 reference strings 760s Checked 9 alignments, 0 edits 760s --------------- 760s PASSED 760s ALSO checking that bowtie2 and bowtie2-align match up 760s Warning: skipping read '37' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '37' because it was < 2 characters long 760s Warning: skipping read '41' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '41' because it was < 2 characters long 760s Warning: skipping read '64' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '64' because it was < 2 characters long 760s Warning: skipping read '66' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '66' because it was < 2 characters long 760s Warning: skipping read '93' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '93' because it was < 2 characters long 760s 93 reads; of these: 760s 93 (100.00%) were unpaired; of these: 760s 84 (90.32%) aligned 0 times 760s 9 (9.68%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 9.68% overall alignment rate 760s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.1 760s Introducing 5 SNPs, 1/1 ref/read gaps, and 2 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutating sequence Sim.pm.2 760s Introducing 6 SNPs, 1/1 ref/read gaps, and 1 rearrangements 760s *** Run 4 of 100 760s /usr/bin/bowtie2 --cp-ival 3 --n-ceil 0.166930295149365,1.37684644643774 --trim3 6 --mp 9.30654496050269,1.68822588422298 --large-index --np 2 --cp-min 2 --rdg 37.6894179156984,10.1785396361611 --mm --score-min L,2.26576875363958,5.11264614834214 --ma 10.8060094637381 -D 16 -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 11 760s Reference gaps introduced: 2 760s Read gaps introduced: 2 760s Rearrangements introduced: 3 760s Created read sampler 760s Sampling 147 reads 760s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 760s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 760s parsing sequence Sim.pm.1... 760s parsing sequence Sim.pm.2... 760s Parsed 76 reference bases 760s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 760s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 760s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '6' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 760s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '9' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 760s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '12' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 760s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '16' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 760s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '20' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 760s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '30' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 760s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '31' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 760s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '33' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 760s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '48' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 760s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '52' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 760s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '53' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 760s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '54' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 760s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '62' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 760s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '63' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 760s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '64' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 760s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '68' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 760s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '69' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 760s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '76' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 760s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '77' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 760s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '86' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 760s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '101' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 760s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '119' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 760s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '121' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 760s Read 50 alignments... 760s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 760s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '132' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 760s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '138' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 760s Read 100 alignments... 760s 147 reads; of these: 760s 147 (100.00%) were unpaired; of these: 760s 125 (85.03%) aligned 0 times 760s 13 (8.84%) aligned exactly 1 time 760s 9 (6.12%) aligned >1 times 760s 14.97% overall alignment rate 760s Read 150 alignments... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CTG 760s CTG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s TGCTC 760s TGCTC 760s Processing line... 760s Processing line... 760s Processing line... 760s CTGG 760s CTGG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s /usr/bin/bowtie2 --cp-ival 3 --n-ceil 0.166930295149365,1.37684644643774 --trim3 6 --mp 9.30654496050269,1.68822588422298 --large-index --np 2 --cp-min 2 --rdg 37.6894179156984,10.1785396361611 --mm --score-min L,2.26576875363958,5.11264614834214 --ma 10.8060094637381 -D 16 -r -p 3 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 760s Processing line... 760s Processing line... 760s GTGGCTGGGGGGTAGGGGCGATTAGTTGG 760s GTGGCTGGGGGGTAGGGGCGATTAGTTGG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CTGGGGGGTAGGGGCGATTAG 760s CTGGGGGGTAGGGGCGATTAG 760s Processing line... 760s CTGGGGGGTAGGG 760s CTGGGGGGTAGGG 760s Processing line... 760s GCTCTCGGTTCGGGGGTGGCTGGG 760s GCTCTCGGTTCGGGGGTGGCTGGG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GG 760s GG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s AGTT 760s AGTT 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GCTCTCGGTTCGGGGGTGGCTGGG 760s GCTCTCGGTTCGGGGGTGGCTGGG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CTGGGGG 760s CTGGGGG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GGGGTAGGGG 760s GGGGTAGGGG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GGGGGTGGCT 760s GGGGGTGGCT 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GATTAGTTGGAG 760s GATTAGTTGGAG 760s Processing line... 760s Processing line... 760s Processing line... 760s GT 760s GT 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CTGGGG 760s CTGGGG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CTGGGGG 760s CTGGGGG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GGGTGGCTGGGG 760s GGGTGGCTGGGG 760s Processing line... 760s Processing line... 760s Processing line... 760s TCGGTTCGGGGGTG 760s TCGGTTCGGGGGTG 760s Processing line... 760s Processing line... 760s Processing line... 760s TGG 760s TGG 760s Processing line... 760s Processing line... 760s GGTTCG 760s GGTTCG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GGGGTGGCT 760s GGGGTGGCT 760s --- Summary --- 760s Read 1 reference strings 760s Checked 22 alignments, 0 edits 760s --------------- 760s PASSED 760s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 760s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 760s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 760s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '6' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 760s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '9' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 760s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '12' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 760s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '16' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 760s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '20' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 760s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '30' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 760s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '31' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 760s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '33' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 760s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '48' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 760s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '52' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 760s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '53' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 760s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '54' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 760s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '62' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 760s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '63' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 760s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '64' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 760s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '68' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 760s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '69' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 760s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '76' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 760s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '77' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 760s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '86' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 760s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '101' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 760s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '119' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 760s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '121' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 760s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '132' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 760s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '138' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 760s 147 reads; of these: 760s 147 (100.00%) were unpaired; of these: 760s 125 (85.03%) aligned 0 times 760s 13 (8.84%) aligned exactly 1 time 760s 9 (6.12%) aligned >1 times 760s 14.97% overall alignment rate 760s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 760s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 760s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.2 760s Introducing 19 SNPs, 1/1 ref/read gaps, and 2 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutating sequence Sim.pm.1 760s Introducing 16 SNPs, 0/1 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 35 760s Reference gaps introduced: 1 760s Read gaps introduced: 2 760s Rearrangements introduced: 2 760s Created read sampler 760s Sampling 104 reads 760s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 760s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 760s parsing sequence Sim.pm.1... 760s parsing sequence Sim.pm.2... 760s Parsed 76 reference bases 760s *** Run 5 of 100 760s /usr/bin/bowtie2 --mp 5.66472847876229,5.57049683550942 -N 1 -L26 --cp-ival 3 --local --trim5 0 --mm -R 2 -k 2 --gbar 3 --score-min L,4.76379733435939,2.0001979270097 --np 1 --cp-min 9 --large-index -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 760s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (1) 760s Warning: skipping mate #1 of read '12' because it was < 2 characters long 760s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (1) 760s Warning: skipping mate #2 of read '14' because it was < 2 characters long 760s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (1) 760s Warning: skipping mate #1 of read '23' because it was < 2 characters long 760s Read 50 alignments... 760s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (1) 760s Warning: skipping mate #2 of read '89' because it was < 2 characters long 760s Read 100 alignments... 760s Read 150 alignments... 760s 104 reads; of these: 760s 104 (100.00%) were paired; of these: 760s 104 (100.00%) aligned concordantly 0 times 760s 0 (0.00%) aligned concordantly exactly 1 time 760s 0 (0.00%) aligned concordantly >1 times 760s ---- 760s 104 pairs aligned concordantly 0 times; of these: 760s 0 (0.00%) aligned discordantly 1 time 760s ---- 760s 104 pairs aligned 0 times concordantly or discordantly; of these: 760s 208 mates make up the pairs; of these: 760s 208 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 0.00% overall alignment rate 760s Read 200 alignments... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s /usr/bin/bowtie2 --mp 5.66472847876229,5.57049683550942 -N 1 -L26 --cp-ival 3 --local --trim5 0 --mm -R 2 -k 2 --gbar 3 --score-min L,4.76379733435939,2.0001979270097 --np 1 --cp-min 9 --large-index -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s --- Summary --- 760s Read 1 reference strings 760s Checked 0 alignments, 0 edits 760s --------------- 760s PASSED 760s ALSO checking that bowtie2 and bowtie2-align match up 760s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (1) 760s Warning: skipping mate #1 of read '12' because it was < 2 characters long 760s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (1) 760s Warning: skipping mate #2 of read '14' because it was < 2 characters long 760s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (1) 760s Warning: skipping mate #1 of read '23' because it was < 2 characters long 760s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (1) 760s Warning: skipping mate #2 of read '89' because it was < 2 characters long 760s 104 reads; of these: 760s 104 (100.00%) were paired; of these: 760s 104 (100.00%) aligned concordantly 0 times 760s 0 (0.00%) aligned concordantly exactly 1 time 760s 0 (0.00%) aligned concordantly >1 times 760s ---- 760s 104 pairs aligned concordantly 0 times; of these: 760s 0 (0.00%) aligned discordantly 1 time 760s ---- 760s 104 pairs aligned 0 times concordantly or discordantly; of these: 760s 208 mates make up the pairs; of these: 760s 208 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 0.00% overall alignment rate 760s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.2 760s Introducing 9 SNPs, 1/0 ref/read gaps, and 1 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutating sequence Sim.pm.1 760s Introducing 17 SNPs, 0/0 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 26 760s Reference gaps introduced: 1 760s Read gaps introduced: 0 760s Rearrangements introduced: 1 760s Created read sampler 760s Sampling 137 reads 760s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 760s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 760s parsing sequence Sim.pm.1... 760s parsing sequence Sim.pm.2... 760s Parsed 76 reference bases 760s *** Run 6 of 100 760s /usr/bin/bowtie2 --large-index --np 2 --cp-min 3 --mm -R 4 --score-min L,7.8064107836899,9.81844619315487 --cp-ival 1 -a --mp 7.86096962875799,3.21119023298434 -N 0 -L15 --trim3 9 --nofw -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 760s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '5' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 760s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '16' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 760s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '29' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 760s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '34' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 760s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '36' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 760s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '42' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 760s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '48' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 760s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '55' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 760s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '56' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 760s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '57' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 760s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '58' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 760s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '60' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 760s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '61' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 760s Read 50 alignments... 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 760s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '68' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 760s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '71' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 760s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '75' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 760s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read '83' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 760s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '90' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 760s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '91' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 760s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '93' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 760s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '97' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 760s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '98' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 760s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '107' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 760s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '108' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 760s Read 100 alignments... 760s Read 150 alignments... 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 760s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '117' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 760s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '119' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 760s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read '123' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 760s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '124' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 760s Read 200 alignments... 761s 137 reads; of these: 761s 110 (80.29%) were paired; of these: 761s 110 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 110 pairs aligned concordantly 0 times; of these: 761s 0 (0.00%) aligned discordantly 1 time 761s ---- 761s 110 pairs aligned 0 times concordantly or discordantly; of these: 761s 220 mates make up the pairs; of these: 761s 210 (95.45%) aligned 0 times 761s 8 (3.64%) aligned exactly 1 time 761s 2 (0.91%) aligned >1 times 761s 27 (19.71%) were unpaired; of these: 761s 24 (88.89%) aligned 0 times 761s 2 (7.41%) aligned exactly 1 time 761s 1 (3.70%) aligned >1 times 761s 5.26% overall alignment rate 761s Read 250 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s CC 761s CC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GGAG 761s GGAG 761s Processing line... 761s Processing line... 761s CC 761s CC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s CC 761s CC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s GGG 761s GGG 761s Processing line... 761s Processing line... 761s AC 761s AC 761s Processing line... 761s CC 761s CC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GGGG 761s GGGG 761s Processing line... 761s GGGG 761s GGGG 761s Processing line... 761s GGGG 761s GGGG 761s Processing line... 761s /usr/bin/bowtie2 --large-index --np 2 --cp-min 3 --mm -R 4 --score-min L,7.8064107836899,9.81844619315487 --cp-ival 1 -a --mp 7.86096962875799,3.21119023298434 -N 0 -L15 --trim3 9 --nofw -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 761s GGGG 761s GGGG 761s Processing line... 761s GGGG 761s GGGG 761s Processing line... 761s GGGG 761s GGGG 761s Processing line... 761s GGGG 761s GGGG 761s Processing line... 761s GGGG 761s GGGG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GGTGGCTGGGGGGTAGGGGCGATTAGTTGGAGTTCT 761s GGTGGCTGGGGGGTAGGGGCGATTAGTTGGAGTTCT 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s CTGGGGGGTAGG 761s CTGGGGGGTAGG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GGTTCGGGGGTGGCTGGGGGG 761s GGTTCGGGGGTGGCTGGGGGG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s AGTTGGA 761s AGTTGGA 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GGC 761s GGC 761s Processing line... 761s GGC 761s GGC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 33 alignments, 0 edits 761s --------------- 761s PASSED 761s ALSO checking that bowtie2 and bowtie2-align match up 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 761s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '5' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 761s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '16' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 761s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '29' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 761s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '34' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 761s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '36' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 761s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '42' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 761s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '48' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 761s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '55' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 761s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '56' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 761s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '57' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 761s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '58' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 761s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '60' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 761s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '61' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 761s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '68' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 761s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '71' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 761s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '75' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 761s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '83' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 761s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '90' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 761s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '91' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 761s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '93' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 761s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '97' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 761s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '98' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 761s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '107' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 761s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '108' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 761s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '117' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 761s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '119' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 761s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '123' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 761s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '124' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 761s 137 reads; of these: 761s 110 (80.29%) were paired; of these: 761s 110 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 110 pairs aligned concordantly 0 times; of these: 761s 0 (0.00%) aligned discordantly 1 time 761s ---- 761s 110 pairs aligned 0 times concordantly or discordantly; of these: 761s 220 mates make up the pairs; of these: 761s 210 (95.45%) aligned 0 times 761s 8 (3.64%) aligned exactly 1 time 761s 2 (0.91%) aligned >1 times 761s 27 (19.71%) were unpaired; of these: 761s 24 (88.89%) aligned 0 times 761s 2 (7.41%) aligned exactly 1 time 761s 1 (3.70%) aligned >1 times 761s 5.26% overall alignment rate 761s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.2 761s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.1 761s Introducing 1 SNPs, 0/3 ref/read gaps, and 1 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 6 761s Reference gaps introduced: 0 761s Read gaps introduced: 3 761s Rearrangements introduced: 1 761s Created read sampler 761s Sampling 88 reads 761s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 761s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 76 reference bases 761s *** Run 7 of 100 761s /usr/bin/bowtie2 --trim3 1 --mp 8.16881575079138,3.33209972746134 -N 0 --local --cp-ival 1 --n-ceil 0.161917361553281,0.488166914551606 --trim5 3 --rdg 49.9774526856297,17.7481434450448 --score-min L,6.11082446827557,9.19856099825245 --gbar 3 --cp-min 13 --large-index -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq 761s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '11' because it was < 2 characters long 761s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '19' because it was < 2 characters long 761s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '22' because it was < 2 characters long 761s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '25' because it was < 2 characters long 761s Warning: skipping mate #2 of read '25' because it was < 2 characters long 761s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '27' because it was < 2 characters long 761s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '28' because it was < 2 characters long 761s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '34' because it was < 2 characters long 761s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '40' because it was < 2 characters long 761s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '61' because it was < 2 characters long 761s Read 50 alignments... 761s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '68' because it was < 2 characters long 761s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '79' because it was < 2 characters long 761s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '83' because it was < 2 characters long 761s 88 reads; of these: 761s 83 (94.32%) were paired; of these: 761s 83 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 83 pairs aligned concordantly 0 times; of these: 761s 0 (0.00%) aligned discordantly 1 time 761s ---- 761s 83 pairs aligned 0 times concordantly or discordantly; of these: 761s 166 mates make up the pairs; of these: 761s 166 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 5 (5.68%) were unpaired; of these: 761s 5 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 0.00% overall alignment rate 761s Read 100 alignments... 761s Read 150 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s /usr/bin/bowtie2 --trim3 1 --mp 8.16881575079138,3.33209972746134 -N 0 --local --cp-ival 1 --n-ceil 0.161917361553281,0.488166914551606 --trim5 3 --rdg 49.9774526856297,17.7481434450448 --score-min L,6.11082446827557,9.19856099825245 --gbar 3 --cp-min 13 --large-index -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 0 alignments, 0 edits 761s --------------- 761s PASSED 761s ALSO checking that bowtie2 and bowtie2-align match up 761s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '11' because it was < 2 characters long 761s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '19' because it was < 2 characters long 761s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '22' because it was < 2 characters long 761s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '25' because it was < 2 characters long 761s Warning: skipping mate #2 of read '25' because it was < 2 characters long 761s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '27' because it was < 2 characters long 761s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '28' because it was < 2 characters long 761s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '34' because it was < 2 characters long 761s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '40' because it was < 2 characters long 761s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '61' because it was < 2 characters long 761s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '68' because it was < 2 characters long 761s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '79' because it was < 2 characters long 761s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '83' because it was < 2 characters long 761s 88 reads; of these: 761s 83 (94.32%) were paired; of these: 761s 83 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 83 pairs aligned concordantly 0 times; of these: 761s 0 (0.00%) aligned discordantly 1 time 761s ---- 761s 83 pairs aligned 0 times concordantly or discordantly; of these: 761s 166 mates make up the pairs; of these: 761s 166 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 5 (5.68%) were unpaired; of these: 761s 5 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 0.00% overall alignment rate 761s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.2 761s Introducing 17 SNPs, 0/2 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.1 761s Introducing 14 SNPs, 0/1 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 31 761s Reference gaps introduced: 0 761s Read gaps introduced: 3 761s Rearrangements introduced: 0 761s Created read sampler 761s Sampling 32 reads 761s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 761s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 76 reference bases 761s *** Run 8 of 100 761s /usr/bin/bowtie2 --large-index --cp-min 9 --trim5 2 --cp-ival 2 --score-min L,4.09998987964314,9.12718323516221 --trim3 3 --ma 17.6359492256565 --mp 6.53454563274811,4.29913937646283 --rfg 15.3070953721661 --mm -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 761s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 761s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '21' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 761s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '22' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 761s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '24' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 761s 32 reads; of these: 761s 29 (90.62%) were paired; of these: 761s 29 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 29 pairs aligned concordantly 0 times; of these: 761s 0 (0.00%) aligned discordantly 1 time 761s ---- 761s 29 pairs aligned 0 times concordantly or discordantly; of these: 761s 58 mates make up the pairs; of these: 761s 49 (84.48%) aligned 0 times 761s 5 (8.62%) aligned exactly 1 time 761s 4 (6.90%) aligned >1 times 761s 3 (9.38%) were unpaired; of these: 761s 3 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 14.75% overall alignment rate 761s Read 50 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s AG 761s AG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GCG 761s GCG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GGTTC 761s GGTTC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GATTAGTTG 761s GATTAGTTG 761s Processing line... 761s Processing line... 761s TAGG 761s TAGG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s AT 761s AT 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GGGG 761s GGGG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s CGGGG 761s CGGGG 761s Processing line... 761s Processing line... 761s TT 761s TT 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 9 alignments, 0 edits 761s --------------- 761s PASSED 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.1 761s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 761s *** Run 9 of 100 761s /usr/bin/bowtie2 --cp-ival 2 --n-ceil 0.210066437188372,0.20943927662556 --norc --trim5 1 --cp-min 6 -M 3 --large-index --rfg 43.5248125021388 -D 40 --score-min L,9.53857863032221,7.08633439118901 -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.2 761s Introducing 15 SNPs, 1/2 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 18 761s Reference gaps introduced: 1 761s Read gaps introduced: 2 761s Rearrangements introduced: 0 761s Created read sampler 761s Sampling 61 reads 761s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 761s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 76 reference bases 761s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 761s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 761s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '17' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 761s 61 reads; of these: 761s 61 (100.00%) were unpaired; of these: 761s 51 (83.61%) aligned 0 times 761s 6 (9.84%) aligned exactly 1 time 761s 4 (6.56%) aligned >1 times 761s 16.39% overall alignment rate 761s Read 50 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GCTCTC 761s GCTCTC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GTAGGGGC 761s GTAGGGGC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s CTGG 761s CTGG 761s Processing line... 761s Processing line... 761s Processing line... 761s TTC 761s TTC 761s Processing line... 761s Processing line... 761s CTG 761s CTG 761s Processing line... 761s Processing line... 761s Processing line... 761s CC 761s CC 761s Processing line... 761s GTAGGGGC 761s GTAGGGGC 761s Processing line... 761s Processing line... 761s Processing line... 761s GGGCGA 761s GGGCGA 761s Processing line... 761s Processing line... 761s GGGCG 761s GGGCG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GC 761s GC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 10 alignments, 0 edits 761s --------------- 761s PASSED 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.2 761s Introducing 10 SNPs, 0/1 ref/read gaps, and 1 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.1 761s Introducing 7 SNPs, 0/2 ref/read gaps, and 2 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 17 761s Reference gaps introduced: 0 761s Read gaps introduced: 3 761s Rearrangements introduced: 3 761s Created read sampler 761s Sampling 241 reads 761s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 761s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 761s parsing sequence Sim.pm.1... 761s *** Run 10 of 100 761s /usr/bin/bowtie2 --mp 6.39020984115444,5.43812910292343 --trim5 2 --cp-ival 2 --local -D 35 -R 1 --score-min L,4.1994160064265,4.02078452509208 --mm --large-index --cp-min 2 --np 10 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq 761s parsing sequence Sim.pm.2... 761s Parsed 76 reference bases 761s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '10' because it was < 2 characters long 761s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '24' because it was < 2 characters long 761s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '25' because it was < 2 characters long 761s Warning: skipping mate #2 of read '25' because it was < 2 characters long 761s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '31' because it was < 2 characters long 761s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '38' because it was < 2 characters long 761s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '50' because it was < 2 characters long 761s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '54' because it was < 2 characters long 761s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '55' because it was < 2 characters long 761s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '57' because it was < 2 characters long 761s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '58' because it was < 2 characters long 761s Read 50 alignments... 761s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '77' because it was < 2 characters long 761s Read 100 alignments... 761s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '82' because it was < 2 characters long 761s Warning: skipping mate #2 of read '93' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '93' because it was < 2 characters long 761s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '136' because it was < 2 characters long 761s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '137' because it was < 2 characters long 761s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '158' because it was < 2 characters long 761s Read 150 alignments... 761s Read 200 alignments... 761s Read 250 alignments... 761s Warning: skipping mate #1 of read '164' because length (0) <= # seed mismatches (0) 761s Read 300 alignments... 761s Warning: skipping mate #1 of read '164' because it was < 2 characters long 761s Warning: skipping mate #1 of read '180' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '180' because it was < 2 characters long 761s Warning: skipping mate #1 of read '189' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '189' because it was < 2 characters long 761s Read 350 alignments... 761s Read 400 alignments... 761s Warning: skipping read '210' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '210' because it was < 2 characters long 761s Warning: skipping mate #1 of read '232' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '232' because it was < 2 characters long 761s Warning: skipping mate #1 of read '235' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '235' because it was < 2 characters long 761s 241 reads; of these: 761s 235 (97.51%) were paired; of these: 761s 235 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 235 pairs aligned concordantly 0 times; of these: 761s 0 (0.00%) aligned discordantly 1 time 761s ---- 761s 235 pairs aligned 0 times concordantly or discordantly; of these: 761s 470 mates make up the pairs; of these: 761s 470 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 6 (2.49%) were unpaired; of these: 761s 6 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 0.00% overall alignment rate 761s Read 450 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 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Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s /usr/bin/bowtie2 --mp 6.39020984115444,5.43812910292343 --trim5 2 --cp-ival 2 --local -D 35 -R 1 --score-min L,4.1994160064265,4.02078452509208 --mm --large-index --cp-min 2 --np 10 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 0 alignments, 0 edits 761s --------------- 761s PASSED 761s ALSO checking that bowtie2 and bowtie2-align match up 761s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '10' because it was < 2 characters long 761s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '24' because it was < 2 characters long 761s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '25' because it was < 2 characters long 761s Warning: skipping mate #2 of read '25' because it was < 2 characters long 761s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '31' because it was < 2 characters long 761s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '38' because it was < 2 characters long 761s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '50' because it was < 2 characters long 761s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '54' because it was < 2 characters long 761s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '55' because it was < 2 characters long 761s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '57' because it was < 2 characters long 761s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '58' because it was < 2 characters long 761s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '77' because it was < 2 characters long 761s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '82' because it was < 2 characters long 761s Warning: skipping mate #2 of read '93' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '93' because it was < 2 characters long 761s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '136' because it was < 2 characters long 761s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '137' because it was < 2 characters long 761s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '158' because it was < 2 characters long 761s Warning: skipping mate #1 of read '164' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '164' because it was < 2 characters long 761s Warning: skipping mate #1 of read '180' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '180' because it was < 2 characters long 761s Warning: skipping mate #1 of read '189' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '189' because it was < 2 characters long 761s Warning: skipping read '210' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '210' because it was < 2 characters long 761s Warning: skipping mate #1 of read '232' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '232' because it was < 2 characters long 761s Warning: skipping mate #1 of read '235' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '235' because it was < 2 characters long 761s 241 reads; of these: 761s 235 (97.51%) were paired; of these: 761s 235 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 235 pairs aligned concordantly 0 times; of these: 761s 0 (0.00%) aligned discordantly 1 time 761s ---- 761s 235 pairs aligned 0 times concordantly or discordantly; of these: 761s 470 mates make up the pairs; of these: 761s 470 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 6 (2.49%) were unpaired; of these: 761s 6 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 0.00% overall alignment rate 761s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.2 761s Introducing 10 SNPs, 0/2 ref/read gaps, and 1 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.1 761s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 10 761s Reference gaps introduced: 0 761s Read gaps introduced: 2 761s Rearrangements introduced: 1 761s Created read sampler 761s Sampling 64 reads 761s *** Run 11 of 100 761s /usr/bin/bowtie2 --cp-ival 2 --local --n-ceil 0.748176978246795,0.477513775736406 --trim5 5 -M 8 --rfg 13.1389952291803,1.05115067416234 --mp 5.68817063863133,4.21088428186493 --cp-min 7 --np 2 --large-index --rdg 44.317602792753 -R 3 --score-min L,8.02198694221158,6.36726203338116 -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw 761s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 761s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 76 reference bases 761s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 761s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '3' because it was < 2 characters long 761s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '15' because it was < 2 characters long 761s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '25' because it was < 2 characters long 761s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '31' because it was < 2 characters long 761s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '40' because it was < 2 characters long 761s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '43' because it was < 2 characters long 761s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '44' because it was < 2 characters long 761s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '46' because it was < 2 characters long 761s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '51' because it was < 2 characters long 761s 64 reads; of these: 761s 64 (100.00%) were unpaired; of these: 761s 64 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 0.00% overall alignment rate 761s Read 50 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 0 alignments, 0 edits 761s --------------- 761s PASSED 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.1 761s Introducing 8 SNPs, 0/1 ref/read gaps, and 4 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.2 761s Introducing 9 SNPs, 1/1 ref/read gaps, and 1 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 17 761s Reference gaps introduced: 1 761s Read gaps introduced: 2 761s Rearrangements introduced: 5 761s Created read sampler 761s Sampling 28 reads 761s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 761s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 76 reference bases 761s *** Run 12 of 100 761s /usr/bin/bowtie2 --rdg 43.9423715882476 --mm --score-min L,4.65250904553722,9.43825918540919 --trim3 4 -i S,1.79220230846535 --cp-ival 1 -a --large-index --np 3 --cp-min 20 --trim5 4 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 761s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 761s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '5' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 761s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '10' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 761s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '12' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 761s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '16' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 761s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '20' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 761s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '21' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 761s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '27' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 761s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '28' because it was < 2 characters long 761s 28 reads; of these: 761s 28 (100.00%) were unpaired; of these: 761s 25 (89.29%) aligned 0 times 761s 3 (10.71%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 10.71% overall alignment rate 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s CTCTCGGTTCGGGGGTGGCTGGGG 761s CTCTCGGTTCGGGGGTGGCTGGGG 761s Processing line... 761s Processing line... 761s GGGGGGTAGGGGC 761s GGGGGGTAGGGGC 761s Processing line... 761s Processing line... 761s Processing line... 761s TTG 761s TTG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 3 alignments, 0 edits 761s --------------- 761s PASSED 761s ALSO checking that bowtie2 and bowtie2-align match up 761s /usr/bin/bowtie2 --rdg 43.9423715882476 --mm --score-min L,4.65250904553722,9.43825918540919 --trim3 4 -i S,1.79220230846535 --cp-ival 1 -a --large-index --np 3 --cp-min 20 --trim5 4 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 761s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 761s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '5' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 761s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '10' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 761s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '12' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 761s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '16' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 761s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '20' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 761s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '21' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 761s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '27' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 761s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '28' because it was < 2 characters long 761s 28 reads; of these: 761s 28 (100.00%) were unpaired; of these: 761s 25 (89.29%) aligned 0 times 761s 3 (10.71%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 10.71% overall alignment rate 761s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.2 761s Introducing 22 SNPs, 0/2 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.1 761s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 31 761s Reference gaps introduced: 0 761s Read gaps introduced: 2 761s Rearrangements introduced: 0 761s Created read sampler 761s Sampling 75 reads 761s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 761s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 76 reference bases 761s *** Run 13 of 100 761s /usr/bin/bowtie2 --cp-ival 2 --large-index --cp-min 2 --trim5 2 --mm --score-min L,9.77585508020021,1.18086456711101 --ma 8.60681482990238 --trim3 7 --gbar 2 --mp 6.75603394595109,3.5563532096753 -i S,1.85834039140443,3.64718428208058 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 761s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 761s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 761s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 761s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 761s Read 50 alignments... 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 761s Read 100 alignments... 761s 75 reads; of these: 761s 62 (82.67%) were paired; of these: 761s 62 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 62 pairs aligned concordantly 0 times; of these: 761s 0 (0.00%) aligned discordantly 1 time 761s ---- 761s 62 pairs aligned 0 times concordantly or discordantly; of these: 761s 124 mates make up the pairs; of these: 761s 115 (92.74%) aligned 0 times 761s 5 (4.03%) aligned exactly 1 time 761s 4 (3.23%) aligned >1 times 761s 13 (17.33%) were unpaired; of these: 761s 11 (84.62%) aligned 0 times 761s 1 (7.69%) aligned exactly 1 time 761s 1 (7.69%) aligned >1 times 761s 8.03% overall alignment rate 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TTC 761s TTC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GGGTGGC 761s GGGTGGC 761s Processing line... 761s Processing line... 761s AGGGG 761s AGGGG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GTTACCTGGGG 761s GTTACCTGGGG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s /usr/bin/bowtie2 --cp-ival 2 --large-index --cp-min 2 --trim5 2 --mm --score-min L,9.77585508020021,1.18086456711101 --ma 8.60681482990238 --trim3 7 --gbar 2 --mp 6.75603394595109,3.5563532096753 -i S,1.85834039140443,3.64718428208058 --qseq -p 4 -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GGGGTG 761s GGGGTG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s ACC 761s ACC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GTGC 761s GTGC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GTGC 761s GTGC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TGGG 761s TGGG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TC 761s TC 761s Processing line... 761s Processing line... 761s TG 761s TG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 11 alignments, 0 edits 761s --------------- 761s PASSED 761s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 761s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 761s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 761s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 761s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 761s 75 reads; of these: 761s 62 (82.67%) were paired; of these: 761s 62 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 62 pairs aligned concordantly 0 times; of these: 761s 0 (0.00%) aligned discordantly 1 time 761s ---- 761s 62 pairs aligned 0 times concordantly or discordantly; of these: 761s 124 mates make up the pairs; of these: 761s 115 (92.74%) aligned 0 times 761s 5 (4.03%) aligned exactly 1 time 761s 4 (3.23%) aligned >1 times 761s 13 (17.33%) were unpaired; of these: 761s 11 (84.62%) aligned 0 times 761s 1 (7.69%) aligned exactly 1 time 761s 1 (7.69%) aligned >1 times 761s 8.03% overall alignment rate 761s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 761s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 761s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 761s /usr/bin/bowtie2 --cp-ival 2 --large-index --cp-min 2 --trim5 2 --mm --score-min L,9.77585508020021,1.18086456711101 --ma 8.60681482990238 --trim3 7 --gbar 2 --mp 6.75603394595109,3.5563532096753 -i S,1.85834039140443,3.64718428208058 --qseq -p 3 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 761s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 761s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 761s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 761s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 761s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 761s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 762s 75 reads; of these: 762s 62 (82.67%) were paired; of these: 762s 62 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 62 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 62 pairs aligned 0 times concordantly or discordantly; of these: 762s 124 mates make up the pairs; of these: 762s 115 (92.74%) aligned 0 times 762s 5 (4.03%) aligned exactly 1 time 762s 4 (3.23%) aligned >1 times 762s 13 (17.33%) were unpaired; of these: 762s 11 (84.62%) aligned 0 times 762s 1 (7.69%) aligned exactly 1 time 762s 1 (7.69%) aligned >1 times 762s 8.03% overall alignment rate 762s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 762s Flattened IUPAC characters 762s Mutating sequence Sim.pm.1 762s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutating sequence Sim.pm.2 762s Introducing 4 SNPs, 2/0 ref/read gaps, and 3 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutated reference genome to subject genome 762s SNPs introduced: 7 762s Reference gaps introduced: 2 762s Read gaps introduced: 0 762s Rearrangements introduced: 3 762s Created read sampler 762s Sampling 172 reads 762s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 762s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 762s parsing sequence Sim.pm.1... 762s parsing sequence Sim.pm.2... 762s *** Run 14 of 100 762s /usr/bin/bowtie2 --large-index --cp-min 3 --np 5 --score-min L,3.01733103742504,4.09017787671886 -D 44 --rdg 4.7287547182963,4.57316642893439 -M 6 --trim5 2 --n-ceil 0.713358409300197,0.161879049967844 --local --cp-ival 1 --rfg 34.8234595879885,1.66125068776603 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 762s Parsed 76 reference bases 762s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 762s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (1) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (1) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_139_139_1/1' because length (0) <= # seed mismatches (0) 762s Read 50 alignments... 762s Read 100 alignments... 762s Warning: skipping read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_154_154_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_154_154_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_163_163_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_163_163_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_167_167_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_167_167_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_171_171_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_171_171_1/1' because it was < 2 characters long 762s /usr/bin/bowtie2 --large-index --cp-min 3 --np 5 --score-min L,3.01733103742504,4.09017787671886 -D 44 --rdg 4.7287547182963,4.57316642893439 -M 6 --trim5 2 --n-ceil 0.713358409300197,0.161879049967844 --local --cp-ival 1 --rfg 34.8234595879885,1.66125068776603 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 762s 172 reads; of these: 762s 172 (100.00%) were unpaired; of these: 762s 172 (100.00%) aligned 0 times 762s 0 (0.00%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 0.00% overall alignment rate 762s Read 150 alignments... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s --- Summary --- 762s Read 1 reference strings 762s Checked 0 alignments, 0 edits 762s --------------- 762s PASSED 762s ALSO checking that bowtie2 and bowtie2-align match up 762s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 762s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (1) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (1) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_139_139_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_154_154_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_154_154_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_163_163_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_163_163_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_167_167_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_167_167_1/1' because it was < 2 characters long 762s Warning: skipping read 'R_1_1_1_171_171_1/1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read 'R_1_1_1_171_171_1/1' because it was < 2 characters long 762s 172 reads; of these: 762s 172 (100.00%) were unpaired; of these: 762s 172 (100.00%) aligned 0 times 762s 0 (0.00%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 0.00% overall alignment rate 762s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 762s Flattened IUPAC characters 762s Mutating sequence Sim.pm.2 762s Introducing 7 SNPs, 3/1 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutating sequence Sim.pm.1 762s Introducing 19 SNPs, 1/0 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutated reference genome to subject genome 762s SNPs introduced: 26 762s Reference gaps introduced: 4 762s Read gaps introduced: 1 762s Rearrangements introduced: 0 762s Created read sampler 762s Sampling 102 reads 762s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 762s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 762s parsing sequence Sim.pm.1... 762s parsing sequence Sim.pm.2... 762s Parsed 76 reference bases 762s *** Run 15 of 100 762s /usr/bin/bowtie2 --large-index --cp-min 8 --np 1 --mm --score-min L,8.86098953251918,4.97744291838382 --cp-ival 3 --n-ceil 0.412156904364627,0.894800114472401 --norc --rfg 43.5149638260584,9.48424640817612 --mp 5.45144857204199,5.25229992179456 -i S,1.00799546934646 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '8' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 762s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '38' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 762s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '46' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 762s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '60' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 762s Read 50 alignments... 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 762s Read 100 alignments... 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 762s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '66' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 762s Warning: skipping mate #1 of read '80' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '80' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 762s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '96' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '96' because it was < 2 characters long 762s Warning: skipping mate #2 of read '96' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 762s 102 reads; of these: 762s 102 (100.00%) were paired; of these: 762s 102 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 102 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 102 pairs aligned 0 times concordantly or discordantly; of these: 762s 204 mates make up the pairs; of these: 762s 197 (96.57%) aligned 0 times 762s 7 (3.43%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 3.43% overall alignment rate 762s Read 150 alignments... 762s Read 200 alignments... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GGGGGTAGGGGC 762s GGGGGTAGGGGC 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GGGGCGATTAG 762s GGGGCGATTAG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TCGGGGGTGGCTGGGGGGTAG 762s TCGGGGGTGGCTGGGGGGTAG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GGGGCGATTAGTTGGAGTTCT 762s GGGGCGATTAGTTGGAGTTCT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GTGGCTGGGGGGTAGGGGCGATTAGTT 762s GTGGCTGGGGGGTAGGGGCGATTAGTT 762s Processing line... 762s Processing line... 762s TCTCGGTTCGGG 762s TCTCGGTTCGGG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GGGGCG 762s GGGGCG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s --- Summary --- 762s Read 1 reference strings 762s Checked 7 alignments, 0 edits 762s --------------- 762s PASSED 762s Flattened IUPAC characters 762s Mutating sequence Sim.pm.1 762s Introducing 17 SNPs, 2/1 ref/read gaps, and 1 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutating sequence Sim.pm.2 762s Introducing 12 SNPs, 1/0 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutated reference genome to subject genome 762s SNPs introduced: 29 762s Reference gaps introduced: 3 762s Read gaps introduced: 1 762s Rearrangements introduced: 1 762s Created read sampler 762s Sampling 94 reads 762s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 762s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 762s parsing sequence Sim.pm.1... 762s parsing sequence Sim.pm.2... 762s Parsed 76 reference bases 762s *** Run 16 of 100 762s /usr/bin/bowtie2 --large-index -a --cp-min 3 --local --cp-ival 2 --score-min L,7.58903138854898,6.51594367430323 --nofw --trim3 0 --mp 7.33038839375741,5.84649289350579 --rfg 30.0352579378509 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq 762s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '8' because it was < 2 characters long 762s Warning: skipping mate #1 of read '11' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '11' because it was < 2 characters long 762s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '18' because it was < 2 characters long 762s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '58' because it was < 2 characters long 762s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '62' because it was < 2 characters long 762s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '64' because it was < 2 characters long 762s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '65' because it was < 2 characters long 762s Read 50 alignments... 762s 94 reads; of these: 762s 94 (100.00%) were paired; of these: 762s 94 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 94 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 94 pairs aligned 0 times concordantly or discordantly; of these: 762s 188 mates make up the pairs; of these: 762s 188 (100.00%) aligned 0 times 762s 0 (0.00%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 0.00% overall alignment rate 762s Read 100 alignments... 762s Read 150 alignments... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s --- Summary --- 762s Read 1 reference strings 762s Checked 0 alignments, 0 edits 762s --------------- 762s PASSED 762s ALSO checking that bowtie2 and bowtie2-align match up 762s /usr/bin/bowtie2 --large-index -a --cp-min 3 --local --cp-ival 2 --score-min L,7.58903138854898,6.51594367430323 --nofw --trim3 0 --mp 7.33038839375741,5.84649289350579 --rfg 30.0352579378509 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 762s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '8' because it was < 2 characters long 762s Warning: skipping mate #1 of read '11' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '11' because it was < 2 characters long 762s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '18' because it was < 2 characters long 762s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '58' because it was < 2 characters long 762s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '62' because it was < 2 characters long 762s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '64' because it was < 2 characters long 762s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '65' because it was < 2 characters long 762s 94 reads; of these: 762s 94 (100.00%) were paired; of these: 762s 94 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 94 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 94 pairs aligned 0 times concordantly or discordantly; of these: 762s 188 mates make up the pairs; of these: 762s 188 (100.00%) aligned 0 times 762s 0 (0.00%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 0.00% overall alignment rate 762s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 762s Flattened IUPAC characters 762s *** Run 17 of 100 762s /usr/bin/bowtie2 --cp-ival 2 --trim5 5 --large-index --cp-min 18 --rfg 14.4174001372787 --mm --rdg 8.92438907156376 --mp 7.07981512266411,4.26643693989475 -R 3 -N 0 -L30 --score-min L,1.97978334002271,1.54474512641473 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq 762s Mutating sequence Sim.pm.1 762s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutating sequence Sim.pm.2 762s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutated reference genome to subject genome 762s SNPs introduced: 3 762s Reference gaps introduced: 2 762s Read gaps introduced: 0 762s Rearrangements introduced: 0 762s Created read sampler 762s Sampling 143 reads 762s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 762s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 762s parsing sequence Sim.pm.1... 762s parsing sequence Sim.pm.2... 762s Parsed 76 reference bases 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '4' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '27' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '29' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 762s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '48' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 762s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '59' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 762s Read 50 alignments... 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 762s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '78' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 762s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '80' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 762s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '83' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 762s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '84' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 762s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '90' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 762s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '99' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 762s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '104' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 762s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '112' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 762s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '113' because it was < 2 characters long 762s Read 100 alignments... 762s Read 150 alignments... 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 762s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '117' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 762s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '118' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 762s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '119' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 762s Warning: skipping mate #2 of read '122' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '122' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 762s Warning: skipping mate #2 of read '127' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '127' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 762s Warning: skipping mate #1 of read '131' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '131' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 762s Warning: skipping read '133' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '133' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 762s 143 reads; of these: 762s 123 (86.01%) were paired; of these: 762s 123 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 123 pairs aligned concordantly 0 times; of these: 762s 1 (0.81%) aligned discordantly 1 time 762s ---- 762s 122 pairs aligned 0 times concordantly or discordantly; of these: 762s 244 mates make up the pairs; of these: 762s 212 (86.89%) aligned 0 times 762s 24 (9.84%) aligned exactly 1 time 762s 8 (3.28%) aligned >1 times 762s 20 (13.99%) were unpaired; of these: 762s 16 (80.00%) aligned 0 times 762s 3 (15.00%) aligned exactly 1 time 762s 1 (5.00%) aligned >1 times 762s 14.29% overall alignment rate 762s Read 200 alignments... 762s Read 250 alignments... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TCTCGGTT 762s TCTCGGTT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GCTGGGGGGTAGGGGCGATTAGTT 762s GCTGGGGGGTAGGGGCGATTAGTT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TTACCT 762s TTACCT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GGGGGTAGGGGCGAT 762s GGGGGTAGGGGCGAT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TGCTCTCGGTTCG 762s TGCTCTCGGTTCG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GG 762s GG 762s Processing line... 762s GCTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGT 762s GCTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CGGTTCGGGGGTGGCTGGGGGGTAGGGGCGAT 762s CGGTTCGGGGGTGGCTGGGGGGTAGGGGCGAT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GGGGTAGGGGCG 762s GGGGTAGGGGCG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TCTCGGTTCGGGGGTG 762s TCTCGGTTCGGGGGTG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GGGCGATTA 762s GGGCGATTA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GGTGGCTGGGGGGTAGGGGCGATTAGT 762s GGTGGCTGGGGGGTAGGGGCGATTAGT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GCTGG 762s GCTGG 762s Processing line... 762s Processing line... 762s ACC 762s ACC 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TGGGGGGTAGGGGCGA 762s TGGGGGGTAGGGGCGA 762s Processing line... 762s Processing line... 762s TCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGAT 762s TCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGAT 762s Processing line... 762s CTCG 762s CTCG 762s Processing line... 762s GGGGGTGGCTGGGGGGTAGGGGCGATTAGTTGGAGTTCT 762s GGGGGTGGCTGGGGGGTAGGGGCGATTAGTTGGAGTTCT 762s Processing line... 762s Processing line... 762s CTGGGGG 762s CTGGGGG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GG 762s GG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GTAGGGGCGATTAGTTGGAG 762s GTAGGGGCGATTAGTTGGAG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GG 762s GG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GGGTGGCTGGGGGGTAGGGGCGATTAGT 762s GGGTGGCTGGGGGGTAGGGGCGATTAGT 762s Processing line... 762s Processing line... 762s TAGGGGCGATTA 762s TAGGGGCGATTA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TGCTCTCGGTTCGGGGGTGGCTGGGGGGTAGGG 762s TGCTCTCGGTTCGGGGGTGGCTGGGGGGTAGGG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GT 762s GT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s AGTTGGAGTTC 762s AGTTGGAGTTC 762s Processing line... 762s GGGG 762s GGGG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GCTGGGGGGTAGGGGCGA 762s GCTGGGGGGTAGGGGCGA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CTCTCGGTTCGGGGGT 762s CTCTCGGTTCGGGGGT 762s Processing line... 762s Processing line... 762s GGGTGGCTGGGGGGTAGGGGCGATTAGTTG 762s GGGTGGCTGGGGGGTAGGGGCGATTAGTTG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s AGGGGCG 762s AGGGGCG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GCTGGGGGGTAGG 762s GCTGGGGGGTAGG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GGGTAGGGGCGATT 762s GGGTAGGGGCGATT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CTCGGTTCGGGGGTGGCTGGGGGGTAGG 762s CTCGGTTCGGGGGTGGCTGGGGGGTAGG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TCT 762s TCT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GGGGTAG 762s GGGGTAG 762s Processing line... 762s Processing line... 762s GCT 762s GCT 762s Processing line... 762s Processing line... 762s Processing line... 762s --- Summary --- 762s Read 1 reference strings 762s Checked 38 alignments, 0 edits 762s --------------- 762s PASSED 762s ALSO checking that bowtie2 and bowtie2-align match up 762s /usr/bin/bowtie2 --cp-ival 2 --trim5 5 --large-index --cp-min 18 --rfg 14.4174001372787 --mm --rdg 8.92438907156376 --mp 7.07981512266411,4.26643693989475 -R 3 -N 0 -L30 --score-min L,1.97978334002271,1.54474512641473 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '4' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '27' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '29' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 762s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '48' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 762s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '59' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 762s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '78' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 762s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '80' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 762s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '83' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 762s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '84' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 762s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '90' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 762s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '99' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 762s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '104' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 762s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '112' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 762s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '113' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 762s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '117' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 762s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '118' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 762s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '119' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 762s Warning: skipping mate #2 of read '122' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '122' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 762s Warning: skipping mate #2 of read '127' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '127' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 762s Warning: skipping mate #1 of read '131' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '131' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 762s Warning: skipping read '133' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '133' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 762s 143 reads; of these: 762s 123 (86.01%) were paired; of these: 762s 123 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 123 pairs aligned concordantly 0 times; of these: 762s 1 (0.81%) aligned discordantly 1 time 762s ---- 762s 122 pairs aligned 0 times concordantly or discordantly; of these: 762s 244 mates make up the pairs; of these: 762s 212 (86.89%) aligned 0 times 762s 24 (9.84%) aligned exactly 1 time 762s 8 (3.28%) aligned >1 times 762s 20 (13.99%) were unpaired; of these: 762s 16 (80.00%) aligned 0 times 762s 3 (15.00%) aligned exactly 1 time 762s 1 (5.00%) aligned >1 times 762s 14.29% overall alignment rate 762s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 762s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 762s /usr/bin/bowtie2 --cp-ival 2 --trim5 5 --large-index --cp-min 18 --rfg 14.4174001372787 --mm --rdg 8.92438907156376 --mp 7.07981512266411,4.26643693989475 -R 3 -N 0 -L30 --score-min L,1.97978334002271,1.54474512641473 -q -p 2 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '4' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '27' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '29' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 762s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '48' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 762s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '59' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 762s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '83' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 762s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '84' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 762s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '90' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 762s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '99' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 762s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '104' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 762s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '112' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 762s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '113' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 762s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '117' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 762s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '118' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 762s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '119' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 762s Warning: skipping mate #2 of read '122' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '122' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 762s Warning: skipping mate #2 of read '127' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '127' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 762s Warning: skipping mate #1 of read '131' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '131' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 762s Warning: skipping read '133' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '133' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 762s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '78' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 762s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '80' because it was < 2 characters long 762s 143 reads; of these: 762s 123 (86.01%) were paired; of these: 762s 123 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 123 pairs aligned concordantly 0 times; of these: 762s 1 (0.81%) aligned discordantly 1 time 762s ---- 762s 122 pairs aligned 0 times concordantly or discordantly; of these: 762s 244 mates make up the pairs; of these: 762s 212 (86.89%) aligned 0 times 762s 24 (9.84%) aligned exactly 1 time 762s 8 (3.28%) aligned >1 times 762s 20 (13.99%) were unpaired; of these: 762s 16 (80.00%) aligned 0 times 762s 3 (15.00%) aligned exactly 1 time 762s 1 (5.00%) aligned >1 times 762s 14.29% overall alignment rate 762s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 762s Flattened IUPAC characters 762s Mutating sequence Sim.pm.1 762s Introducing 18 SNPs, 0/2 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutating sequence Sim.pm.2 762s Introducing 10 SNPs, 1/0 ref/read gaps, and 2 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutated reference genome to subject genome 762s SNPs introduced: 28 762s Reference gaps introduced: 1 762s Read gaps introduced: 2 762s Rearrangements introduced: 2 762s Created read sampler 762s Sampling 55 reads 762s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 762s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 762s parsing sequence Sim.pm.1... 762s *** Run 18 of 100 762s /usr/bin/bowtie2 -M 5 --norc --cp-ival 1 --mp 6.51385696589846,5.78876389099515 -i S -N 0 -L26 --rfg 37.9786974425378,14.9268506559461 --large-index --np 4 --cp-min 3 --score-min L,5.43658967414411,1.9135749189434 --ma 21.2180132114008 --mm --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 762s parsing sequence Sim.pm.2... 762s Parsed 76 reference bases 762s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 762s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 763s Read 50 alignments... 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 763s 55 reads; of these: 763s 55 (100.00%) were paired; of these: 763s 55 (100.00%) aligned concordantly 0 times 763s 0 (0.00%) aligned concordantly exactly 1 time 763s 0 (0.00%) aligned concordantly >1 times 763s ---- 763s 55 pairs aligned concordantly 0 times; of these: 763s 0 (0.00%) aligned discordantly 1 time 763s ---- 763s 55 pairs aligned 0 times concordantly or discordantly; of these: 763s 110 mates make up the pairs; of these: 763s 105 (95.45%) aligned 0 times 763s 1 (0.91%) aligned exactly 1 time 763s 4 (3.64%) aligned >1 times 763s 4.55% overall alignment rate 763s Read 100 alignments... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CG 763s CG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s ACCTGGG 763s ACCTGGG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GT 763s GT 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s *** Run 19 of 100 763s /usr/bin/bowtie2 -a --large-index --cp-min 3 --cp-ival 6 --score-min L,3.90481289378791,7.39533336023024 -D 29 -i L,0.0985323641799628 -R 2 --mp 9.76822853288587,5.31199088064918 --rfg 3.58865535959401,6.09105079003578 --mm -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s TC 763s TC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CT 763s CT 763s Processing line... 763s --- Summary --- 763s Read 1 reference strings 763s Checked 5 alignments, 0 edits 763s --------------- 763s PASSED 763s Flattened IUPAC characters 763s Mutating sequence Sim.pm.2 763s Introducing 12 SNPs, 2/0 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutating sequence Sim.pm.1 763s Introducing 0 SNPs, 2/1 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutated reference genome to subject genome 763s SNPs introduced: 12 763s Reference gaps introduced: 4 763s Read gaps introduced: 1 763s Rearrangements introduced: 0 763s Created read sampler 763s Sampling 93 reads 763s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 763s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 763s parsing sequence Sim.pm.1... 763s parsing sequence Sim.pm.2... 763s Parsed 76 reference bases 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 763s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read '2' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 763s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read '7' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 763s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read '19' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 763s Read 50 alignments... 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 763s Read 100 alignments... 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 763s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read '65' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 763s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read '77' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 763s Warning: skipping mate #1 of read '78' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read '78' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 763s Read 150 alignments... 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 763s Read 200 alignments... 763s 93 reads; of these: 763s 93 (100.00%) were paired; of these: 763s 92 (98.92%) aligned concordantly 0 times 763s 0 (0.00%) aligned concordantly exactly 1 time 763s 1 (1.08%) aligned concordantly >1 times 763s ---- 763s 92 pairs aligned concordantly 0 times; of these: 763s 0 (0.00%) aligned discordantly 1 time 763s ---- 763s 92 pairs aligned 0 times concordantly or discordantly; of these: 763s 184 mates make up the pairs; of these: 763s 167 (90.76%) aligned 0 times 763s 5 (2.72%) aligned exactly 1 time 763s 12 (6.52%) aligned >1 times 763s 10.22% overall alignment rate 763s Read 250 alignments... 763s Read 300 alignments... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s Processing line... 763s AG 763s AG 763s Processing line... 763s AG 763s AG 763s Processing line... 763s AG 763s AG 763s Processing line... 763s CT 763s CT 763s Processing line... 763s CT 763s CT 763s Processing line... 763s CT 763s CT 763s Processing line... 763s CT 763s CT 763s Processing line... 763s CT 763s CT 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s AGTTGGAG 763s AGTTGGAG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GA 763s GA 763s Processing line... 763s TC 763s TC 763s Processing line... 763s TC 763s TC 763s Processing line... 763s TC 763s TC 763s Processing line... 763s GA 763s GA 763s Processing line... 763s TC 763s TC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s ACC 763s ACC 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s ACC 763s ACC 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s Processing line... 763s CCT 763s CCT 763s Processing line... 763s AGG 763s AGG 763s Processing line... 763s TTAG 763s TTAG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s ACC 763s ACC 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s GGT 763s GGT 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GGC 763s GGC 763s Processing line... 763s GGC 763s GGC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GGGGGTGGCTGGGGG 763s GGGGGTGGCTGGGGG 763s Processing line... 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s CC 763s CC 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GGTTCGGGGGTGGC 763s GGTTCGGGGGTGGC 763s Processing line... 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GATTAGTTGGAGTT 763s GATTAGTTGGAGTT 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GT 763s GT 763s Processing line... 763s GT 763s GT 763s Processing line... 763s GT 763s GT 763s Processing line... 763s GT 763s GT 763s Processing line... 763s GT 763s GT 763s Processing line... 763s GT 763s GT 763s Processing line... 763s GT 763s GT 763s Processing line... 763s AC 763s AC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s GGG 763s GGG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GGTTC 763s GGTTC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s --- Summary --- 763s Read 1 reference strings 763s Checked 138 alignments, 0 edits 763s --------------- 763s PASSED 763s Flattened IUPAC characters 763s Mutating sequence Sim.pm.1 763s Introducing 3 SNPs, 1/1 ref/read gaps, and 3 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutating sequence Sim.pm.2 763s Introducing 14 SNPs, 3/1 ref/read gaps, and 2 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutated reference genome to subject genome 763s SNPs introduced: 17 763s Reference gaps introduced: 4 763s Read gaps introduced: 2 763s Rearrangements introduced: 5 763s Created read sampler 763s Sampling 29 reads 763s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 763s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 763s parsing sequence Sim.pm.1... 763s parsing sequence Sim.pm.2... 763s Parsed 76 reference bases 763s *** Run 20 of 100 763s /usr/bin/bowtie2 --cp-min 4 --np 6 --large-index --score-min L,7.96249646172496,3.93906031214638 -R 2 --rdg 36.9519239607796,19.3750982139648 --mm --n-ceil 1.44672943603806,0.0704861590598354 --local --cp-ival 2 --trim3 8 -i S,0.969418419245894 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 763s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 763s 29 reads; of these: 763s 29 (100.00%) were unpaired; of these: 763s 29 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s /usr/bin/bowtie2 --cp-min 4 --np 6 --large-index --score-min L,7.96249646172496,3.93906031214638 -R 2 --rdg 36.9519239607796,19.3750982139648 --mm --n-ceil 1.44672943603806,0.0704861590598354 --local --cp-ival 2 --trim3 8 -i S,0.969418419245894 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s --- Summary --- 763s Read 1 reference strings 763s Checked 0 alignments, 0 edits 763s --------------- 763s PASSED 763s ALSO checking that bowtie2 and bowtie2-align match up 763s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 763s 29 reads; of these: 763s 29 (100.00%) were unpaired; of these: 763s 29 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 763s /usr/bin/bowtie2 --cp-min 4 --np 6 --large-index --score-min L,7.96249646172496,3.93906031214638 -R 2 --rdg 36.9519239607796,19.3750982139648 --mm --n-ceil 1.44672943603806,0.0704861590598354 --local --cp-ival 2 --trim3 8 -i S,0.969418419245894 --qseq -p 4 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 763s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 763s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 763s 29 reads; of these: 763s 29 (100.00%) were unpaired; of these: 763s 29 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 763s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 763s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 763s Flattened IUPAC characters 763s Mutating sequence Sim.pm.1 763s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutating sequence Sim.pm.2 763s Introducing 25 SNPs, 0/0 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutated reference genome to subject genome 763s SNPs introduced: 25 763s Reference gaps introduced: 0 763s Read gaps introduced: 1 763s Rearrangements introduced: 0 763s Created read sampler 763s Sampling 99 reads 763s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 763s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 763s parsing sequence Sim.pm.1... 763s parsing sequence Sim.pm.2... 763s Parsed 76 reference bases 763s *** Run 21 of 100 763s /usr/bin/bowtie2 --rfg 45.8557605714256 -N 1 -L13 --mp 6.13583366691408,4.83014850344631 --trim3 5 --cp-ival 1 --mm -D 21 -k 6 --ma 23.9619759101271 --score-min L,1.73053939691551,9.5710658824726 --cp-min 4 --large-index -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw 763s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 763s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 763s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '2' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 763s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '6' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 763s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '8' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 763s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '13' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 763s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '17' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 763s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '25' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 763s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '29' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 763s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '32' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 763s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '39' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 763s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '54' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 763s Warning: skipping read '61' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '61' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 763s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '81' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 763s Warning: skipping read '84' because length (1) <= # seed mismatches (1) 763s Warning: skipping read '84' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 763s 99 reads; of these: 763s 99 (100.00%) were unpaired; of these: 763s 92 (92.93%) aligned 0 times 763s 5 (5.05%) aligned exactly 1 time 763s 2 (2.02%) aligned >1 times 763s 7.07% overall alignment rate 763s Read 50 alignments... 763s Read 100 alignments... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CGGGGGTGGCT 763s CGGGGGTGGCT 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s GG 763s GG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s AGT 763s AGT 763s Processing line... 763s AGT 763s AGT 763s Processing line... 763s GGCG 763s GGCG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GTGG 763s GTGG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s TTAGTTGGAGTT 763s TTAGTTGGAGTT 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s TCGGTTC 763s TCGGTTC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s --- Summary --- 763s Read 1 reference strings 763s Checked 13 alignments, 0 edits 763s --------------- 763s PASSED 763s ALSO checking that bowtie2 and bowtie2-align match up 763s /usr/bin/bowtie2 --rfg 45.8557605714256 -N 1 -L13 --mp 6.13583366691408,4.83014850344631 --trim3 5 --cp-ival 1 --mm -D 21 -k 6 --ma 23.9619759101271 --score-min L,1.73053939691551,9.5710658824726 --cp-min 4 --large-index -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 763s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 763s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 763s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '2' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 763s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '6' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 763s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '8' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 763s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '13' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 763s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '17' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 763s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '25' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 763s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '29' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 763s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '32' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 763s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '39' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 763s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '54' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 763s Warning: skipping read '61' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '61' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 763s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 763s Warning: skipping read '81' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 763s Warning: skipping read '84' because length (1) <= # seed mismatches (1) 763s Warning: skipping read '84' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 763s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 763s 99 reads; of these: 763s 99 (100.00%) were unpaired; of these: 763s 92 (92.93%) aligned 0 times 763s 5 (5.05%) aligned exactly 1 time 763s 2 (2.02%) aligned >1 times 763s 7.07% overall alignment rate 763s Flattened IUPAC characters 763s Mutating sequence Sim.pm.1 763s Introducing 21 SNPs, 1/0 ref/read gaps, and 1 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s *** Run 22 of 100 763s /usr/bin/bowtie2 --score-min L,2.02065038343672,8.17531806272549 -D 20 -k 6 --mm --np 5 --cp-min 6 --large-index --mp 9.71988286179958,5.35448842641502 --norc --trim5 4 --local --cp-ival 2 -q -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq 763s Finished read gaps 763s Mutating sequence Sim.pm.2 763s Introducing 13 SNPs, 2/0 ref/read gaps, and 3 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutated reference genome to subject genome 763s SNPs introduced: 34 763s Reference gaps introduced: 3 763s Read gaps introduced: 0 763s Rearrangements introduced: 4 763s Created read sampler 763s Sampling 96 reads 763s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 763s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 763s parsing sequence Sim.pm.1... 763s parsing sequence Sim.pm.2... 763s Parsed 76 reference bases 763s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '7' because it was < 2 characters long 763s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '22' because it was < 2 characters long 763s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '23' because it was < 2 characters long 763s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '36' because it was < 2 characters long 763s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '47' because it was < 2 characters long 763s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '50' because it was < 2 characters long 763s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '52' because it was < 2 characters long 763s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '62' because it was < 2 characters long 763s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '64' because it was < 2 characters long 763s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '69' because it was < 2 characters long 763s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '92' because it was < 2 characters long 763s 96 reads; of these: 763s 96 (100.00%) were unpaired; of these: 763s 96 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s Read 50 alignments... 763s Read 100 alignments... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s /usr/bin/bowtie2 --score-min L,2.02065038343672,8.17531806272549 -D 20 -k 6 --mm --np 5 --cp-min 6 --large-index --mp 9.71988286179958,5.35448842641502 --norc --trim5 4 --local --cp-ival 2 -q -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s --- Summary --- 763s Read 1 reference strings 763s Checked 0 alignments, 0 edits 763s --------------- 763s PASSED 763s ALSO checking that bowtie2 and bowtie2-align match up 763s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '7' because it was < 2 characters long 763s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '22' because it was < 2 characters long 763s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '23' because it was < 2 characters long 763s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '36' because it was < 2 characters long 763s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '47' because it was < 2 characters long 763s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '50' because it was < 2 characters long 763s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '52' because it was < 2 characters long 763s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '62' because it was < 2 characters long 763s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '64' because it was < 2 characters long 763s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '69' because it was < 2 characters long 763s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '92' because it was < 2 characters long 763s 96 reads; of these: 763s 96 (100.00%) were unpaired; of these: 763s 96 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 763s /usr/bin/bowtie2 --score-min L,2.02065038343672,8.17531806272549 -D 20 -k 6 --mm --np 5 --cp-min 6 --large-index --mp 9.71988286179958,5.35448842641502 --norc --trim5 4 --local --cp-ival 2 -q -p 3 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 763s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 763s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '7' because it was < 2 characters long 763s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '22' because it was < 2 characters long 763s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '23' because it was < 2 characters long 763s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '36' because it was < 2 characters long 763s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '47' because it was < 2 characters long 763s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '50' because it was < 2 characters long 763s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '52' because it was < 2 characters long 763s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '62' because it was < 2 characters long 763s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '64' because it was < 2 characters long 763s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '69' because it was < 2 characters long 763s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '92' because it was < 2 characters long 763s 96 reads; of these: 763s 96 (100.00%) were unpaired; of these: 763s 96 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 763s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 763s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 763s /usr/bin/bowtie2 --score-min L,2.02065038343672,8.17531806272549 -D 20 -k 6 --mm --np 5 --cp-min 6 --large-index --mp 9.71988286179958,5.35448842641502 --norc --trim5 4 --local --cp-ival 2 -q -p 2 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 763s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 764s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '7' because it was < 2 characters long 764s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '22' because it was < 2 characters long 764s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '23' because it was < 2 characters long 764s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 764s Warning: skipping read '36' because it was < 2 characters long 764s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '47' because it was < 2 characters long 764s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '50' because it was < 2 characters long 764s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '52' because it was < 2 characters long 764s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 764s Warning: skipping read '62' because it was < 2 characters long 764s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '64' because it was < 2 characters long 764s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '69' because it was < 2 characters long 764s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '92' because it was < 2 characters long 764s 96 reads; of these: 764s 96 (100.00%) were unpaired; of these: 764s 96 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 0.00% overall alignment rate 764s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 764s Flattened IUPAC characters 764s Mutating sequence Sim.pm.1 764s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutating sequence Sim.pm.2 764s Introducing 7 SNPs, 4/3 ref/read gaps, and 1 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutated reference genome to subject genome 764s SNPs introduced: 11 764s Reference gaps introduced: 4 764s Read gaps introduced: 3 764s Rearrangements introduced: 1 764s Created read sampler 764s Sampling 69 reads 764s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 764s *** Run 23 of 100 764s /usr/bin/bowtie2 -R 1 --mp 7.26956239105799,1.12392537041272 --ma 3.25334751537747 --score-min L,7.86736930009275,1.57403057105495 --rfg 36.8634591057869 --mm --rdg 49.5356980243392,2.7826898878108 --trim5 2 --cp-min 2 --large-index --cp-ival 1 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 764s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 764s parsing sequence Sim.pm.1... 764s parsing sequence Sim.pm.2... 764s Parsed 76 reference bases 764s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 764s 69 reads; of these: 764s 69 (100.00%) were unpaired; of these: 764s 62 (89.86%) aligned 0 times 764s 4 (5.80%) aligned exactly 1 time 764s 3 (4.35%) aligned >1 times 764s 10.14% overall alignment rate 764s Read 50 alignments... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s CGGTTCGGGGGTGGC 764s CGGTTCGGGGGTGGC 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s GGTAGGG 764s GGTAGGG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s /usr/bin/bowtie2 -R 1 --mp 7.26956239105799,1.12392537041272 --ma 3.25334751537747 --score-min L,7.86736930009275,1.57403057105495 --rfg 36.8634591057869 --mm --rdg 49.5356980243392,2.7826898878108 --trim5 2 --cp-min 2 --large-index --cp-ival 1 --qseq -p 3 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s GGTAGGG 764s GGTAGGG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s TG 764s TG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s GG 764s GG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s GGGCG 764s GGGCG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s TGC 764s TGC 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s --- Summary --- 764s Read 1 reference strings 764s Checked 7 alignments, 0 edits 764s --------------- 764s PASSED 764s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 764s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 764s 69 reads; of these: 764s 69 (100.00%) were unpaired; of these: 764s 62 (89.86%) aligned 0 times 764s 4 (5.80%) aligned exactly 1 time 764s 3 (4.35%) aligned >1 times 764s 10.14% overall alignment rate 764s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 764s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 764s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 764s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 764s /usr/bin/bowtie2 -R 1 --mp 7.26956239105799,1.12392537041272 --ma 3.25334751537747 --score-min L,7.86736930009275,1.57403057105495 --rfg 36.8634591057869 --mm --rdg 49.5356980243392,2.7826898878108 --trim5 2 --cp-min 2 --large-index --cp-ival 1 --qseq -p 4 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 764s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 764s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 764s 69 reads; of these: 764s 69 (100.00%) were unpaired; of these: 764s 62 (89.86%) aligned 0 times 764s 4 (5.80%) aligned exactly 1 time 764s 3 (4.35%) aligned >1 times 764s 10.14% overall alignment rate 764s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 764s Flattened IUPAC characters 764s Mutating sequence Sim.pm.2 764s Introducing 25 SNPs, 0/0 ref/read gaps, and 1 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutating sequence Sim.pm.1 764s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutated reference genome to subject genome 764s SNPs introduced: 32 764s Reference gaps introduced: 0 764s Read gaps introduced: 0 764s Rearrangements introduced: 1 764s Created read sampler 764s Sampling 134 reads 764s *** Run 24 of 100 764s /usr/bin/bowtie2 --cp-min 5 --np 1 --large-index --score-min L,8.70887908956722,6.88105488982502 -k 2 --gbar 3 --mm --trim5 3 --local --cp-ival 1 --trim3 2 --rfg 11.9042352004256 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 764s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 764s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 764s parsing sequence Sim.pm.1... 764s parsing sequence Sim.pm.2... 764s Parsed 76 reference bases 764s Warning: skipping mate #2 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 764s Warning: skipping mate #2 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 764s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 764s Warning: skipping mate #2 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 764s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 764s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 764s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 764s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 764s Warning: skipping mate #2 of read 'R_1_1_1_126_126_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 764s Read 50 alignments... 764s Read 100 alignments... 764s Read 150 alignments... 764s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 764s Warning: skipping mate #1 of read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 764s 134 reads; of these: 764s 122 (91.04%) were paired; of these: 764s 122 (100.00%) aligned concordantly 0 times 764s 0 (0.00%) aligned concordantly exactly 1 time 764s 0 (0.00%) aligned concordantly >1 times 764s ---- 764s 122 pairs aligned concordantly 0 times; of these: 764s 0 (0.00%) aligned discordantly 1 time 764s ---- 764s 122 pairs aligned 0 times concordantly or discordantly; of these: 764s 244 mates make up the pairs; of these: 764s 244 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 12 (8.96%) were unpaired; of these: 764s 12 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 0.00% overall alignment rate 764s Read 200 alignments... 764s Read 250 alignments... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s --- Summary --- 764s Read 1 reference strings 764s Checked 0 alignments, 0 edits 764s --------------- 764s PASSED 764s Flattened IUPAC characters 764s Mutating sequence Sim.pm.1 764s Introducing 8 SNPs, 0/2 ref/read gaps, and 0 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutating sequence Sim.pm.2 764s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutated reference genome to subject genome 764s SNPs introduced: 8 764s Reference gaps introduced: 0 764s Read gaps introduced: 2 764s Rearrangements introduced: 0 764s Created read sampler 764s Sampling 102 reads 764s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 764s *** Run 25 of 100 764s /usr/bin/bowtie2 --score-min L,9.67038682055794,9.42862220920291 --ma 11.5768843153655 -k 3 --gbar 1 -N 1 -L14 --mp 8.71249310232788,5.78641420455892 --rfg 37.2335706780914,2.51261226533542 --large-index --cp-min 11 --trim5 9 --cp-ival 1 -q -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq 764s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 764s parsing sequence Sim.pm.1... 764s parsing sequence Sim.pm.2... 764s Parsed 76 reference bases 764s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 764s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 764s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '6' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 764s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '8' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 764s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '9' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 764s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '11' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 764s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '17' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 764s Warning: skipping read '23' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '23' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 764s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '29' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 764s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '39' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 764s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '42' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 764s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '46' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 764s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '47' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 764s Warning: skipping read '50' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '50' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 764s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '51' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 764s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '70' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 764s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '77' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 764s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '83' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 764s Warning: skipping read '91' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '91' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 764s Warning: skipping read '94' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '94' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 764s Warning: skipping read '95' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '95' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 764s Warning: skipping read '98' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '98' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 764s Warning: skipping read '100' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '100' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 764s Warning: skipping read '101' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '101' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 764s Warning: skipping read '102' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '102' because it was < 2 characters long 764s 102 reads; of these: 764s 102 (100.00%) were unpaired; of these: 764s 89 (87.25%) aligned 0 times 764s 7 (6.86%) aligned exactly 1 time 764s 6 (5.88%) aligned >1 times 764s 12.75% overall alignment rate 764s Read 50 alignments... 764s Read 100 alignments... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s TCGGGGGTGGCTG 764s TCGGGGGTGGCTG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s TTAGTTGGAGTT 764s TTAGTTGGAGTT 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s GG 764s GG 764s Processing line... 764s CC 764s CC 764s Processing line... 764s GG 764s GG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s CCTGG 764s CCTGG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s TG 764s TG 764s Processing line... 764s TG 764s TG 764s Processing line... 764s /usr/bin/bowtie2 --score-min L,9.67038682055794,9.42862220920291 --ma 11.5768843153655 -k 3 --gbar 1 -N 1 -L14 --mp 8.71249310232788,5.78641420455892 --rfg 37.2335706780914,2.51261226533542 --large-index --cp-min 11 --trim5 9 --cp-ival 1 -q -p 3 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 764s TG 764s TG 764s Processing line... 764s Processing line... 764s AGT 764s AGT 764s Processing line... 764s AGT 764s AGT 764s Processing line... 764s Processing line... 764s Processing line... 764s GT 764s GT 764s Processing line... 764s GT 764s GT 764s Processing line... 764s GT 764s GT 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s GGGG 764s GGGG 764s Processing line... 764s GGGG 764s GGGG 764s Processing line... 764s GGGG 764s GGGG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s GGTTA 764s GGTTA 764s Processing line... 764s GCG 764s GCG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s CTCT 764s CTCT 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s AGGGGCGATTAGTTGGAGTTCT 764s AGGGGCGATTAGTTGGAGTTCT 764s Processing line... 764s GGT 764s GGT 764s Processing line... 764s GGT 764s GGT 764s Processing line... 764s GGT 764s GGT 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s --- Summary --- 764s Read 1 reference strings 764s Checked 24 alignments, 0 edits 764s --------------- 764s PASSED 764s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 764s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 764s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 764s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '6' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 764s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '8' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 764s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '9' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 764s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '11' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 764s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '17' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 764s Warning: skipping read '23' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '23' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 764s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '29' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 764s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '39' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 764s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '42' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 764s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '46' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 764s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '47' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 764s Warning: skipping read '50' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '50' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 764s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '51' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 764s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '70' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 764s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '77' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 764s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '83' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 764s Warning: skipping read '91' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '91' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 764s Warning: skipping read '94' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '94' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 764s Warning: skipping read '95' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '95' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 764s Warning: skipping read '98' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '98' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 764s Warning: skipping read '100' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '100' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 764s Warning: skipping read '101' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '101' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 764s Warning: skipping read '102' because length (0) <= # seed mismatches (1) 764s Warning: skipping read '102' because it was < 2 characters long 764s 102 reads; of these: 764s 102 (100.00%) were unpaired; of these: 764s 89 (87.25%) aligned 0 times 764s 7 (6.86%) aligned exactly 1 time 764s 6 (5.88%) aligned >1 times 764s 12.75% overall alignment rate 764s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 764s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 764s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 764s Flattened IUPAC characters 764s Mutating sequence Sim.pm.1 764s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutating sequence Sim.pm.2 764s Introducing 6 SNPs, 2/1 ref/read gaps, and 3 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutated reference genome to subject genome 764s SNPs introduced: 10 764s Reference gaps introduced: 2 764s Read gaps introduced: 1 764s Rearrangements introduced: 3 764s Created read sampler 764s Sampling 97 reads 764s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 764s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 764s parsing sequence Sim.pm.1... 764s parsing sequence Sim.pm.2... 764s Parsed 76 reference bases 764s *** Run 26 of 100 764s /usr/bin/bowtie2 --nofw --trim3 1 -i C,2.6143260147505 --mp 4.37315809713604,2.67486644692889 --local --cp-ival 2 --score-min L,9.95811468942079,8.33661469473143 -k 2 --gbar 2 --rdg 28.9653380685736 --mm --large-index --cp-min 10 --np 1 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 765s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '1' because it was < 2 characters long 765s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '12' because it was < 2 characters long 765s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '20' because it was < 2 characters long 765s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '35' because it was < 2 characters long 765s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '38' because it was < 2 characters long 765s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '47' because it was < 2 characters long 765s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '59' because it was < 2 characters long 765s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '88' because it was < 2 characters long 765s 97 reads; of these: 765s 96 (98.97%) were paired; of these: 765s 96 (100.00%) aligned concordantly 0 times 765s 0 (0.00%) aligned concordantly exactly 1 time 765s 0 (0.00%) aligned concordantly >1 times 765s ---- 765s 96 pairs aligned concordantly 0 times; of these: 765s 0 (0.00%) aligned discordantly 1 time 765s ---- 765s 96 pairs aligned 0 times concordantly or discordantly; of these: 765s 192 mates make up the pairs; of these: 765s 192 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 1 (1.03%) were unpaired; of these: 765s 1 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 0.00% overall alignment rate 765s Read 50 alignments... 765s Read 100 alignments... 765s Read 150 alignments... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s --- Summary --- 765s Read 1 reference strings 765s Checked 0 alignments, 0 edits 765s --------------- 765s PASSED 765s ALSO checking that bowtie2 and bowtie2-align match up 765s /usr/bin/bowtie2 --nofw --trim3 1 -i C,2.6143260147505 --mp 4.37315809713604,2.67486644692889 --local --cp-ival 2 --score-min L,9.95811468942079,8.33661469473143 -k 2 --gbar 2 --rdg 28.9653380685736 --mm --large-index --cp-min 10 --np 1 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 765s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '1' because it was < 2 characters long 765s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '12' because it was < 2 characters long 765s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '20' because it was < 2 characters long 765s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '35' because it was < 2 characters long 765s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '38' because it was < 2 characters long 765s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '47' because it was < 2 characters long 765s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '59' because it was < 2 characters long 765s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '88' because it was < 2 characters long 765s 97 reads; of these: 765s 96 (98.97%) were paired; of these: 765s 96 (100.00%) aligned concordantly 0 times 765s 0 (0.00%) aligned concordantly exactly 1 time 765s 0 (0.00%) aligned concordantly >1 times 765s ---- 765s 96 pairs aligned concordantly 0 times; of these: 765s 0 (0.00%) aligned discordantly 1 time 765s ---- 765s 96 pairs aligned 0 times concordantly or discordantly; of these: 765s 192 mates make up the pairs; of these: 765s 192 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 1 (1.03%) were unpaired; of these: 765s 1 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 0.00% overall alignment rate 765s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 765s Flattened IUPAC characters 765s Mutating sequence Sim.pm.2 765s Introducing 3 SNPs, 2/0 ref/read gaps, and 5 rearrangements 765s Finished SNPs 765s Finished ref gaps 765s Finished read gaps 765s Mutating sequence Sim.pm.1 765s Introducing 11 SNPs, 0/0 ref/read gaps, and 0 rearrangements 765s Finished SNPs 765s Finished ref gaps 765s Finished read gaps 765s Mutated reference genome to subject genome 765s SNPs introduced: 14 765s Reference gaps introduced: 2 765s Read gaps introduced: 0 765s Rearrangements introduced: 5 765s Created read sampler 765s Sampling 117 reads 765s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 765s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 765s parsing sequence Sim.pm.1... 765s parsing sequence Sim.pm.2... 765s Parsed 76 reference bases 765s *** Run 27 of 100 765s /usr/bin/bowtie2 --large-index --cp-min 2 --cp-ival 1 -N 0 -L18 --mp 8.53625789824032,7.21717313884744 --score-min L,2.66759251372207,8.49136325380107 --trim3 7 -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw 765s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 765s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '0' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 765s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '3' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 765s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '9' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 765s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '12' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 765s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '13' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 765s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 765s Warning: skipping read '20' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 765s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '22' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 765s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '28' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 765s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 765s Warning: skipping read '32' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 765s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '43' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 765s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '47' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 765s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '48' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 765s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '54' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 765s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '56' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 765s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '71' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 765s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 765s Warning: skipping read '77' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 765s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '81' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 765s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '84' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 765s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '85' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 765s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '88' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 765s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '95' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 765s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '100' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 765s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '103' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 765s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '107' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 765s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '108' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 765s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '116' because it was < 2 characters long 765s 117 reads; of these: 765s 117 (100.00%) were unpaired; of these: 765s 98 (83.76%) aligned 0 times 765s 14 (11.97%) aligned exactly 1 time 765s 5 (4.27%) aligned >1 times 765s 16.24% overall alignment rate 765s Read 50 alignments... 765s Read 100 alignments... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GCGA 765s GCGA 765s Processing line... 765s Processing line... 765s Processing line... 765s CTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGT 765s CTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGT 765s Processing line... 765s Processing line... 765s Processing line... 765s GGGGTGGCTGGGGGG 765s GGGGTGGCTGGGGGG 765s Processing line... 765s GCT 765s GCT 765s Processing line... 765s Processing line... 765s CTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGT 765s CTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGT 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GTAG 765s GTAG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GTGGCTGGGGGGTAGGGGC 765s GTGGCTGGGGGGTAGGGGC 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GGAG 765s GGAG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GGTTCGGGGG 765s GGTTCGGGGG 765s Processing line... 765s Processing line... 765s Processing line... 765s GCTCTCGGTTCGG 765s GCTCTCGGTTCGG 765s Processing line... 765s Processing line... 765s GG 765s GG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GGGG 765s GGGG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GTT 765s GTT 765s Processing line... 765s Processing line... 765s GGC 765s GGC 765s Processing line... 765s Processing line... 765s Processing line... 765s TTGGAG 765s TTGGAG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GTGGCTGGGGGGTAGGGGCGAT 765s GTGGCTGGGGGGTAGGGGCGAT 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s CTCGGTTCGGGGGTGGCTGGGGGGTA 765s CTCGGTTCGGGGGTGGCTGGGGGGTA 765s Processing line... 765s GGTGG 765s GGTGG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s TCGGTT 765s TCGGTT 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s --- Summary --- 765s Read 1 reference strings 765s Checked 19 alignments, 0 edits 765s --------------- 765s PASSED 765s /usr/bin/bowtie2 --large-index --cp-min 2 --cp-ival 1 -N 0 -L18 --mp 8.53625789824032,7.21717313884744 --score-min L,2.66759251372207,8.49136325380107 --trim3 7 -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 765s ALSO checking that bowtie2 and bowtie2-align match up 765s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 765s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '0' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 765s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '3' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 765s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '9' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 765s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '12' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 765s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '13' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 765s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 765s Warning: skipping read '20' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 765s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '22' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 765s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '28' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 765s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 765s Warning: skipping read '32' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 765s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '43' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 765s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '47' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 765s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '48' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 765s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '54' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 765s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '56' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 765s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '71' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 765s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 765s Warning: skipping read '77' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 765s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '81' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 765s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '84' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 765s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '85' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 765s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '88' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 765s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '95' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 765s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '100' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 765s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '103' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 765s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '107' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 765s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '108' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 765s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '116' because it was < 2 characters long 765s 117 reads; of these: 765s 117 (100.00%) were unpaired; of these: 765s 98 (83.76%) aligned 0 times 765s 14 (11.97%) aligned exactly 1 time 765s 5 (4.27%) aligned >1 times 765s 16.24% overall alignment rate 765s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 765s /usr/bin/bowtie2 --large-index --cp-min 2 --cp-ival 1 -N 0 -L18 --mp 8.53625789824032,7.21717313884744 --score-min L,2.66759251372207,8.49136325380107 --trim3 7 -r -p 4 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 765s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 765s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 765s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '0' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 765s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '3' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 765s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '9' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 765s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '12' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 765s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '13' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 765s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 765s Warning: skipping read '20' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 765s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '22' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 765s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '28' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 765s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 765s Warning: skipping read '32' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 765s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '43' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 765s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '47' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 765s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '48' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 765s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '54' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 765s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '56' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 765s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '71' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 765s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 765s Warning: skipping read '77' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 765s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '81' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 765s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '84' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 765s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '85' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 765s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '88' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 765s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '95' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 765s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '116' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 765s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '100' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 765s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '103' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 765s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '107' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 765s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '108' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 765s 117 reads; of these: 765s 117 (100.00%) were unpaired; of these: 765s 98 (83.76%) aligned 0 times 765s 14 (11.97%) aligned exactly 1 time 765s 5 (4.27%) aligned >1 times 765s 16.24% overall alignment rate 765s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 765s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 765s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 765s /usr/bin/bowtie2 --large-index --cp-min 2 --cp-ival 1 -N 0 -L18 --mp 8.53625789824032,7.21717313884744 --score-min L,2.66759251372207,8.49136325380107 --trim3 7 -r -p 2 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 765s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 765s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 765s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '0' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 765s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '3' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 765s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '9' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 765s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '12' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 765s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '13' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 765s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 765s Warning: skipping read '20' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 765s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '22' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 765s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '28' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 765s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 765s Warning: skipping read '32' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 765s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '43' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 765s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '47' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 765s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '48' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 765s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '54' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 765s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '56' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 765s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '71' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 765s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 765s Warning: skipping read '77' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 765s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '81' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 765s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '84' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 765s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '85' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 765s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '88' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 765s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '95' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 765s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '100' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 765s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '103' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 765s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '107' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 765s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '108' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 765s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 765s Warning: skipping read '116' because it was < 2 characters long 765s 117 reads; of these: 765s 117 (100.00%) were unpaired; of these: 765s 98 (83.76%) aligned 0 times 765s 14 (11.97%) aligned exactly 1 time 765s 5 (4.27%) aligned >1 times 765s 16.24% overall alignment rate 765s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 765s Flattened IUPAC characters 765s Mutating sequence Sim.pm.2 765s Introducing 22 SNPs, 0/0 ref/read gaps, and 2 rearrangements 765s Finished SNPs 765s Finished ref gaps 765s Finished read gaps 765s Mutating sequence Sim.pm.1 765s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 765s Finished SNPs 765s Finished ref gaps 765s Finished read gaps 765s Mutated reference genome to subject genome 765s SNPs introduced: 32 765s Reference gaps introduced: 0 765s Read gaps introduced: 0 765s Rearrangements introduced: 2 765s Created read sampler 765s Sampling 18 reads 765s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 765s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 765s parsing sequence Sim.pm.1... 765s parsing sequence Sim.pm.2... 765s Parsed 76 reference bases 765s *** Run 28 of 100 765s /usr/bin/bowtie2 --cp-ival 4 --cp-min 2 --np 2 -a --large-index --trim3 1 --ma 22.092612693958 --score-min L,3.92045948944942,9.95352557210702 -D 7 -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw 765s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 765s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 765s 18 reads; of these: 765s 18 (100.00%) were unpaired; of these: 765s 15 (83.33%) aligned 0 times 765s 1 (5.56%) aligned exactly 1 time 765s 2 (11.11%) aligned >1 times 765s 16.67% overall alignment rate 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s TCGGTTCG 765s TCGGTTCG 765s Processing line... 765s TGG 765s TGG 765s Processing line... 765s TGG 765s TGG 765s Processing line... 765s TGG 765s TGG 765s Processing line... 765s TGG 765s TGG 765s Processing line... 765s TGG 765s TGG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s TA 765s TA 765s Processing line... 765s TA 765s TA 765s Processing line... 765s TA 765s TA 765s Processing line... 765s TA 765s TA 765s Processing line... 765s TA 765s TA 765s Processing line... 765s TA 765s TA 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s --- Summary --- 765s Read 1 reference strings 765s Checked 12 alignments, 0 edits 765s --------------- 765s PASSED 765s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 765s /usr/bin/bowtie2 --cp-ival 4 --cp-min 2 --np 2 -a --large-index --trim3 1 --ma 22.092612693958 --score-min L,3.92045948944942,9.95352557210702 -D 7 -r -p 3 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 766s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 766s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 766s 18 reads; of these: 766s 18 (100.00%) were unpaired; of these: 766s 15 (83.33%) aligned 0 times 766s 1 (5.56%) aligned exactly 1 time 766s 2 (11.11%) aligned >1 times 766s 16.67% overall alignment rate 766s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 766s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 766s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 766s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 766s /usr/bin/bowtie2 --cp-ival 4 --cp-min 2 --np 2 -a --large-index --trim3 1 --ma 22.092612693958 --score-min L,3.92045948944942,9.95352557210702 -D 7 -r -p 4 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 766s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 766s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 766s 18 reads; of these: 766s 18 (100.00%) were unpaired; of these: 766s 15 (83.33%) aligned 0 times 766s 1 (5.56%) aligned exactly 1 time 766s 2 (11.11%) aligned >1 times 766s 16.67% overall alignment rate 766s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 766s Flattened IUPAC characters 766s Mutating sequence Sim.pm.2 766s Introducing 10 SNPs, 1/1 ref/read gaps, and 1 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutating sequence Sim.pm.1 766s Introducing 1 SNPs, 3/1 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutated reference genome to subject genome 766s SNPs introduced: 11 766s Reference gaps introduced: 4 766s Read gaps introduced: 2 766s Rearrangements introduced: 1 766s Created read sampler 766s Sampling 10 reads 766s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 766s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 766s parsing sequence Sim.pm.1... 766s parsing sequence Sim.pm.2... 766s Parsed 76 reference bases 766s *** Run 29 of 100 766s /usr/bin/bowtie2 -D 42 --gbar 2 --score-min L,5.76669761639521,8.02384845401492 --rdg 10.8440383289676,9.28072551212351 --cp-min 4 --np 3 --large-index -i C,3.03406580020468 -N 0 -L26 --mp 8.82923495093592,1.66025992721417 --trim3 6 --rfg 16.5487918004614,9.57812081377035 -a --cp-ival 1 --local --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 766s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 766s 10 reads; of these: 766s 10 (100.00%) were unpaired; of these: 766s 10 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s /usr/bin/bowtie2 -D 42 --gbar 2 --score-min L,5.76669761639521,8.02384845401492 --rdg 10.8440383289676,9.28072551212351 --cp-min 4 --np 3 --large-index -i C,3.03406580020468 -N 0 -L26 --mp 8.82923495093592,1.66025992721417 --trim3 6 --rfg 16.5487918004614,9.57812081377035 -a --cp-ival 1 --local --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 766s Processing line... 766s --- Summary --- 766s Read 1 reference strings 766s Checked 0 alignments, 0 edits 766s --------------- 766s PASSED 766s ALSO checking that bowtie2 and bowtie2-align match up 766s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 766s 10 reads; of these: 766s 10 (100.00%) were unpaired; of these: 766s 10 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 766s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 766s /usr/bin/bowtie2 -D 42 --gbar 2 --score-min L,5.76669761639521,8.02384845401492 --rdg 10.8440383289676,9.28072551212351 --cp-min 4 --np 3 --large-index -i C,3.03406580020468 -N 0 -L26 --mp 8.82923495093592,1.66025992721417 --trim3 6 --rfg 16.5487918004614,9.57812081377035 -a --cp-ival 1 --local --qseq -p 2 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 766s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 766s 10 reads; of these: 766s 10 (100.00%) were unpaired; of these: 766s 10 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 766s Flattened IUPAC characters 766s Mutating sequence Sim.pm.2 766s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutating sequence Sim.pm.1 766s Introducing 6 SNPs, 1/1 ref/read gaps, and 1 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutated reference genome to subject genome 766s SNPs introduced: 6 766s Reference gaps introduced: 1 766s Read gaps introduced: 1 766s Rearrangements introduced: 1 766s Created read sampler 766s Sampling 146 reads 766s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 766s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 766s parsing sequence Sim.pm.1... 766s *** Run 30 of 100 766s /usr/bin/bowtie2 --local --cp-ival 2 --cp-min 3 -a --large-index --rfg 16.0182609407009 --mm --trim3 7 --score-min L,1.56137018777265,9.06482199044427 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 766s parsing sequence Sim.pm.2... 766s Parsed 76 reference bases 766s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '3' because it was < 2 characters long 766s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '6' because it was < 2 characters long 766s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 766s Warning: skipping read '7' because it was < 2 characters long 766s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '10' because it was < 2 characters long 766s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '17' because it was < 2 characters long 766s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '18' because it was < 2 characters long 766s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '31' because it was < 2 characters long 766s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '33' because it was < 2 characters long 766s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '35' because it was < 2 characters long 766s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '39' because it was < 2 characters long 766s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '52' because it was < 2 characters long 766s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '57' because it was < 2 characters long 766s Warning: skipping mate #2 of read '62' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '62' because it was < 2 characters long 766s Read 50 alignments... 766s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '68' because it was < 2 characters long 766s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '69' because it was < 2 characters long 766s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '74' because it was < 2 characters long 766s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '76' because it was < 2 characters long 766s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '79' because it was < 2 characters long 766s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '97' because it was < 2 characters long 766s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '100' because it was < 2 characters long 766s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '108' because it was < 2 characters long 766s Warning: skipping mate #1 of read '109' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '109' because it was < 2 characters long 766s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '110' because it was < 2 characters long 766s Warning: skipping mate #1 of read '117' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '117' because it was < 2 characters long 766s Warning: skipping mate #2 of read '118' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '118' because it was < 2 characters long 766s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '123' because it was < 2 characters long 766s Warning: skipping mate #1 of read '139' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '139' because it was < 2 characters long 766s Read 100 alignments... 766s Read 150 alignments... 766s 146 Read 200 alignments... 766s reads; of these: 766s 121 (82.88%) were paired; of these: 766s 121 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 121 pairs aligned concordantly 0 times; of these: 766s 0 (0.00%) aligned discordantly 1 time 766s ---- 766s 121 pairs aligned 0 times concordantly or discordantly; of these: 766s 242 mates make up the pairs; of these: 766s 242 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 25 (17.12%) were unpaired; of these: 766s 25 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s Read 250 alignments... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing 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line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s --- Summary --- 766s Read 1 reference strings 766s Checked 0 alignments, 0 edits 766s --------------- 766s PASSED 766s Flattened IUPAC characters 766s Mutating sequence Sim.pm.1 766s Introducing 2 SNPs, 3/2 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutating sequence Sim.pm.2 766s Introducing 0 SNPs, 3/2 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutated reference genome to subject genome 766s SNPs introduced: 2 766s Reference gaps introduced: 6 766s Read gaps introduced: 4 766s Rearrangements introduced: 0 766s Created read sampler 766s Sampling 162 reads 766s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 766s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 766s parsing sequence Sim.pm.1... 766s parsing sequence Sim.pm.2... 766s Parsed 76 reference bases 766s *** Run 31 of 100 766s /usr/bin/bowtie2 --score-min L,1.69441348501721,9.24922430337596 --gbar 1 --rdg 20.066794913112,13.8387254305611 --mm --large-index --cp-min 3 --np 7 --trim5 9 --cp-ival 1 -q -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq 766s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 766s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '7' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 766s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '12' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 766s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '13' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 766s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '19' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 766s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '21' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 766s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '25' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 766s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '27' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 766s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '29' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 766s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '36' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 766s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '38' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 766s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '44' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 766s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '45' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 766s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '54' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 766s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 766s Warning: skipping read '59' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 766s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '63' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 766s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '69' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 766s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '71' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 766s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '72' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 766s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '75' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 766s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '82' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 766s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '88' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 766s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '94' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 766s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '96' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 766s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '98' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 766s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '107' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 766s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '118' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 766s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '119' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 766s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '121' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 766s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '124' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 766s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '130' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 766s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '134' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 766s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '135' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 766s Warning: skipping read '140' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '140' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 766s Warning: skipping read '148' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '148' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 766s Warning: skipping read '153' because length (1) <= # seed mismatches (0) 766s Warning: skipping read '153' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 766s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '156' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 766s Warning: skipping read '157' because length (1) <= # seed mismatches (0) 766s Warning: skipping read '157' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 766s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '158' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 766s Warning: skipping read '159' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '159' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 766s Read 50 alignments... 766s Read 100 alignments... 766s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 766s 162 reads; of these: 766s 162 (100.00%) were unpaired; of these: 766s 150 (92.59%) aligned 0 times 766s 10 (6.17%) aligned exactly 1 time 766s 2 (1.23%) aligned >1 times 766s 7.41% overall alignment rate 766s Read 150 alignments... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s TCTCGGTTC 766s TCTCGGTTC 766s Processing line... 766s Processing line... 766s Processing line... 766s GAG 766s GAG 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s GCTG 766s GCTG 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s GTGC 766s GTGC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s GTTCGGGGG 766s GTTCGGGGG 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s GTTCGGGGGTGGCTGGGGGGTAGG 766s GTTCGGGGGTGGCTGGGGGGTAGG 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s GGGGTAGGG 766s GGGGTAGGG 766s Processing line... 766s Processing line... 766s GGGGG 766s GGGGG 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s GGCG 766s GGCG 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s TGGC 766s TGGC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s GATTAGTTGGAG 766s GATTAGTTGGAG 766s Processing line... 766s CTCGGTTCGGGGGTGGCTGGGGGGT 766s CTCGGTTCGGGGGTGGCTGGGGGGT 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s --- Summary --- 766s Read 1 reference strings 766s Checked 12 alignments, 0 edits 766s --------------- 766s PASSED 766s Flattened IUPAC characters 766s Mutating sequence Sim.pm.1 766s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutating sequence Sim.pm.2 766s Introducing 16 SNPs, 2/0 ref/read gaps, and 1 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutated reference genome to subject genome 766s SNPs introduced: 24 766s Reference gaps introduced: 2 766s Read gaps introduced: 0 766s Rearrangements introduced: 2 766s Created read sampler 766s Sampling 119 reads 766s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 766s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 766s parsing sequence Sim.pm.1... 766s parsing sequence Sim.pm.2... 766s Parsed 76 reference bases 766s *** Run 32 of 100 766s /usr/bin/bowtie2 --score-min L,2.62404573803949,6.4015937192065 -k 9 --rdg 35.6675446120749 --large-index --cp-min 2 --np 1 --trim5 1 --local --cp-ival 1 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 766s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 766s Warning: skipping mate #2 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 766s Warning: skipping mate #2 of read 'R_1_1_1_101_101_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 766s Warning: skipping mate #2 of read 'R_1_1_1_110_110_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 766s Read 50 alignments... 766s Read 100 alignments... 766s Read 150 alignments... 766s 119 reads; of these: 766s 116 (97.48%) were paired; of these: 766s 116 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 116 pairs aligned concordantly 0 times; of these: 766s 0 (0.00%) aligned discordantly 1 time 766s ---- 766s 116 pairs aligned 0 times concordantly or discordantly; of these: 766s 232 mates make up the pairs; of these: 766s 232 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 3 (2.52%) were unpaired; of these: 766s 3 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s Read 200 alignments... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s --- Summary --- 766s Read 1 reference strings 766s Checked 0 alignments, 0 edits 766s --------------- 766s PASSED 766s ALSO checking that bowtie2 and bowtie2-align match up 766s /usr/bin/bowtie2 --score-min L,2.62404573803949,6.4015937192065 -k 9 --rdg 35.6675446120749 --large-index --cp-min 2 --np 1 --trim5 1 --local --cp-ival 1 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 766s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 766s Warning: skipping mate #2 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 766s Warning: skipping mate #2 of read 'R_1_1_1_101_101_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 766s Warning: skipping mate #2 of read 'R_1_1_1_110_110_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 766s 119 reads; of these: 766s 116 (97.48%) were paired; of these: 766s 116 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 116 pairs aligned concordantly 0 times; of these: 766s 0 (0.00%) aligned discordantly 1 time 766s ---- 766s 116 pairs aligned 0 times concordantly or discordantly; of these: 766s 232 mates make up the pairs; of these: 766s 232 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 3 (2.52%) were unpaired; of these: 766s 3 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 766s /usr/bin/bowtie2 --score-min L,2.62404573803949,6.4015937192065 -k 9 --rdg 35.6675446120749 --large-index --cp-min 2 --np 1 --trim5 1 --local --cp-ival 1 --qseq -p 3 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 766s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 766s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 766s Warning: skipping mate #2 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 766s Warning: skipping mate #2 of read 'R_1_1_1_101_101_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 766s Warning: skipping mate #2 of read 'R_1_1_1_110_110_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 766s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 766s 119 reads; of these: 766s 116 (97.48%) were paired; of these: 766s 116 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 116 pairs aligned concordantly 0 times; of these: 766s 0 (0.00%) aligned discordantly 1 time 766s ---- 766s 116 pairs aligned 0 times concordantly or discordantly; of these: 766s 232 mates make up the pairs; of these: 766s 232 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 3 (2.52%) were unpaired; of these: 766s 3 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 766s *** Run 33 of 100 766s /usr/bin/bowtie2 --score-min L,3.12372428202842,1.79096363821622 -R 2 --rdg 38.319703088689 --mm --np 2 --cp-min 3 --large-index -a --trim5 0 --norc --local --cp-ival 1 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 766s Flattened IUPAC characters 766s Mutating sequence Sim.pm.1 766s Introducing 12 SNPs, 0/0 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutating sequence Sim.pm.2 766s Introducing 9 SNPs, 1/5 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutated reference genome to subject genome 766s SNPs introduced: 21 766s Reference gaps introduced: 1 766s Read gaps introduced: 5 766s Rearrangements introduced: 0 766s Created read sampler 766s Sampling 45 reads 766s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 766s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 766s parsing sequence Sim.pm.1... 766s parsing sequence Sim.pm.2... 766s Parsed 76 reference bases 767s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '10' because it was < 2 characters long 767s 45 reads; of these: 767s 45 (100.00%) were paired; of these: 767s 45 (100.00%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 45 pairs aligned concordantly 0 times; of these: 767s 0 (0.00%) aligned discordantly 1 time 767s ---- 767s 45 pairs aligned 0 times concordantly or discordantly; of these: 767s 90 mates make up the pairs; of these: 767s 89 (98.89%) aligned 0 times 767s 1 (1.11%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 1.11% overall alignment rate 767s Read 50 alignments... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TGGCTGGGGGGTAGG 767s TGGCTGGGGGGTAGG 767s Processing line... 767s --- Summary --- 767s Read 1 reference strings 767s Checked 1 alignments, 0 edits 767s --------------- 767s PASSED 767s ALSO checking that bowtie2 and bowtie2-align match up 767s /usr/bin/bowtie2 --score-min L,3.12372428202842,1.79096363821622 -R 2 --rdg 38.319703088689 --mm --np 2 --cp-min 3 --large-index -a --trim5 0 --norc --local --cp-ival 1 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 767s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '10' because it was < 2 characters long 767s 45 reads; of these: 767s 45 (100.00%) were paired; of these: 767s 45 (100.00%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 45 pairs aligned concordantly 0 times; of these: 767s 0 (0.00%) aligned discordantly 1 time 767s ---- 767s 45 pairs aligned 0 times concordantly or discordantly; of these: 767s 90 mates make up the pairs; of these: 767s 89 (98.89%) aligned 0 times 767s 1 (1.11%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 1.11% overall alignment rate 767s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 767s Flattened IUPAC characters 767s Mutating sequence Sim.pm.1 767s Introducing 1 SNPs, 0/2 ref/read gaps, and 2 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutating sequence Sim.pm.2 767s Introducing 12 SNPs, 2/0 ref/read gaps, and 1 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutated reference genome to subject genome 767s SNPs introduced: 13 767s Reference gaps introduced: 2 767s Read gaps introduced: 2 767s Rearrangements introduced: 3 767s Created read sampler 767s Sampling 83 reads 767s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 767s *** Run 34 of 100 767s /usr/bin/bowtie2 --cp-min 4 --large-index --trim5 8 --cp-ival 2 --ma 29.5342350264126 --score-min L,5.26529142379285,3.5401035905391 -D 29 --gbar 1 --rdg 30.7916551536371,8.70016185497574 --mm --rfg 24.2517457243048 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 767s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 767s parsing sequence Sim.pm.1... 767s parsing sequence Sim.pm.2... 767s Parsed 76 reference bases 767s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 767s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 767s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 767s Read 50 alignments... 767s 83 reads; of these: 767s 63 (75.90%) were paired; of these: 767s 63 (100.00%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 63 pairs aligned concordantly 0 times; of these: 767s 0 (0.00%) aligned discordantly 1 time 767s ---- 767s 63 pairs aligned 0 times concordantly or discordantly; of these: 767s 126 mates make up the pairs; of these: 767s 116 (92.06%) aligned 0 times 767s 4 (3.17%) aligned exactly 1 time 767s 6 (4.76%) aligned >1 times 767s 20 (24.10%) were unpaired; of these: 767s 18 (90.00%) aligned 0 times 767s 1 (5.00%) aligned exactly 1 time 767s 1 (5.00%) aligned >1 times 767s 8.22% overall alignment rate 767s Read 100 alignments... 767s Read 150 alignments... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TT 767s TT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GGC 767s GGC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GGGTGGCTGGGGGGT 767s GGGTGGCTGGGGGGT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GGGT 767s GGGT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GGTGG 767s GGTGG 767s Processing line... 767s Processing line... 767s GGTA 767s GGTA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TGGGGG 767s TGGGGG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TG 767s TG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GCTCTC 767s GCTCTC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s /usr/bin/bowtie2 --cp-min 4 --large-index --trim5 8 --cp-ival 2 --ma 29.5342350264126 --score-min L,5.26529142379285,3.5401035905391 -D 29 --gbar 1 --rdg 30.7916551536371,8.70016185497574 --mm --rfg 24.2517457243048 --qseq -p 4 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 767s Processing line... 767s Processing line... 767s TGC 767s TGC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GAGT 767s GAGT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TGCTCTCGGTTCG 767s TGCTCTCGGTTCG 767s Processing line... 767s Processing line... 767s --- Summary --- 767s Read 1 reference strings 767s Checked 12 alignments, 0 edits 767s --------------- 767s PASSED 767s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 767s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 767s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 767s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 767s 83 reads; of these: 767s 63 (75.90%) were paired; of these: 767s 63 (100.00%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 63 pairs aligned concordantly 0 times; of these: 767s 0 (0.00%) aligned discordantly 1 time 767s ---- 767s 63 pairs aligned 0 times concordantly or discordantly; of these: 767s 126 mates make up the pairs; of these: 767s 116 (92.06%) aligned 0 times 767s 4 (3.17%) aligned exactly 1 time 767s 6 (4.76%) aligned >1 times 767s 20 (24.10%diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 767s ) were unpaired; of these: 767s 18 (90.00%) aligned 0 times 767s 1 (5.00%) aligned exactly 1 time 767s 1 (5.00%) aligned >1 times 767s 8.22% overall alignment rate 767s Flattened IUPAC characters 767s Mutating sequence Sim.pm.2 767s Introducing 10 SNPs, 2/2 ref/read gaps, and 0 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutating sequence Sim.pm.1 767s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutated reference genome to subject genome 767s SNPs introduced: 12 767s Reference gaps introduced: 2 767s Read gaps introduced: 3 767s Rearrangements introduced: 0 767s Created read sampler 767s Sampling 39 reads 767s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 767s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 767s parsing sequence Sim.pm.1... 767s parsing sequence Sim.pm.2... 767s Parsed 76 reference bases 767s *** Run 35 of 100 767s /usr/bin/bowtie2 --large-index --np 1 --cp-min 10 -D 21 --score-min L,9.18432276773613,4.70006871619534 --mm --rdg 18.7163367275561,1.70080277070787 --norc -M 8 --cp-ival 2 --local --trim3 3 --nofw --rfg 32.445558480859 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 767s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 767s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '4' because it was < 2 characters long 767s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '17' because it was < 2 characters long 767s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '26' because it was < 2 characters long 767s 39 reads; of these: 767s 39 (100.00%) were unpaired; of these: 767s 39 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 0.00% overall alignment rate 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s --- Summary --- 767s Read 1 reference strings 767s Checked 0 alignments, 0 edits 767s --------------- 767s PASSED 767s ALSO checking that bowtie2 and bowtie2-align match up 767s /usr/bin/bowtie2 --large-index --np 1 --cp-min 10 -D 21 --score-min L,9.18432276773613,4.70006871619534 --mm --rdg 18.7163367275561,1.70080277070787 --norc -M 8 --cp-ival 2 --local --trim3 3 --nofw --rfg 32.445558480859 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 767s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 767s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '4' because it was < 2 characters long 767s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '17' because it was < 2 characters long 767s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '26' because it was < 2 characters long 767s 39 reads; of these: 767s 39 (100.00%) were unpaired; of these: 767s 39 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 767s /usr/bin/bowtie2 --large-index --np 1 --cp-min 10 -D 21 --score-min L,9.18432276773613,4.70006871619534 --mm --rdg 18.7163367275561,1.70080277070787 --norc -M 8 --cp-ival 2 --local --trim3 3 --nofw --rfg 32.445558480859 -f -p 2 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 767s 0.00%) aligned >1 times 767s 0.00% overall alignment rate 767s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 767s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 767s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '4' because it was < 2 characters long 767s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '17' because it was < 2 characters long 767s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '26' because it was < 2 characters long 767s 39sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 767s reads; of these: 767s 39 (100.00%) were unpaired; of these: 767s 39 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 0.00% overall alignment rate 767s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 767s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 767s /usr/bin/bowtie2 --large-index --np 1 --cp-min 10 -D 21 --score-min L,9.18432276773613,4.70006871619534 --mm --rdg 18.7163367275561,1.70080277070787 --norc -M 8 --cp-ival 2 --local --trim3 3 --nofw --rfg 32.445558480859 -f -p 4 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 767s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 767s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 767s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '4' because it was < 2 characters long 767s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '17' because it was < 2 characters long 767s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '26' because it was < 2 characters long 767s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 767s *** Run 36 of 100 767s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 1.47764569176356,0.337742498474248 --trim5 6 -a --rfg 14.56638140238 --mp 3.79974443417894,3.06339735881834 --cp-min 4 --large-index --mm --rdg 17.5450909963496,18.0115068806233 --score-min L,1.04380954835741,1.48380237218142 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 767s 39 reads; of these: 767s 39 (100.00%) were unpaired; of these: 767s 39 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 0.00% overall alignment rate 767s Flattened IUPAC characters 767s Mutating sequence Sim.pm.2 767s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutating sequence Sim.pm.1 767s Introducing 0 SNPs, 0/1 ref/read gaps, and 1 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutated reference genome to subject genome 767s SNPs introduced: 1 767s Reference gaps introduced: 1 767s Read gaps introduced: 1 767s Rearrangements introduced: 1 767s Created read sampler 767s Sampling 80 reads 767s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 767s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 767s parsing sequence Sim.pm.1... 767s parsing sequence Sim.pm.2... 767s Parsed 76 reference bases 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 767s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 767s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '6' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 767s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '38' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 767s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '53' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 767s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '60' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 767s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '68' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 767s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '73' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 767s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '75' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 767s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '77' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 767s Warning: skipping mate #1 of read '78' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '78' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 767s Read 50 alignments... 767s Read 100 alignments... 767s 80 reads; of these: 767s 71 (88.75%) were paired; of these: 767s 70 (98.59%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 1 (1.41%) aligned concordantly >1 times 767s ---- 767s 70 pairs aligned concordantly 0 times; of these: 767s 1 (1.43%) aligned discordantly 1 time 767s ---- 767s 69 pairs aligned 0 times concordantly or discordantly; of these: 767s 138 mates make up the pairs; of these: 767s 123 (89.13%) aligned 0 times 767s 11 (7.97%) aligned exactly 1 time 767s 4 (2.90%) aligned >1 times 767s 9 (11.25%) were unpaired; of these: 767s 7 (77.78%) aligned 0 times 767s 1 (11.11%) aligned exactly 1 time 767s 1 (11.11%) aligned >1 times 767s 13.91% overall alignment rate 767s Read 150 alignments... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GGAGT 767s GGAGT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GGGGCGATTAGTT 767s GGGGCGATTAGTT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CTGGGGGGTAG 767s CTGGGGGGTAG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s GGG 767s GGG 767s Processing line... 767s Processing line... 767s GCTGGGGGGTAG 767s GCTGGGGGGTAG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TCG 767s TCG 767s Processing line... 767s CGA 767s CGA 767s Processing line... 767s TCG 767s TCG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GGGGTA 767s GGGGTA 767s Processing line... 767s Processing line... 767s GGTTC 767s GGTTC 767s Processing line... 767s Processing line... 767s GGTGGC 767s GGTGGC 767s Processing line... 767s CGGGGGTGGCTGGGGGG 767s CGGGGGTGGCTGGGGGG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GGGGC 767s GGGGC 767s Processing line... 767s TGGGGGGTAGGGGCGATTAGTTGGAGTT 767s TGGGGGGTAGGGGCGATTAGTTGGAGTT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GGGGG 767s GGGGG 767s Processing line... 767s GGGGG 767s GGGGG 767s Processing line... 767s GGGGG 767s GGGGG 767s Processing line... 767s GGGGG 767s GGGGG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GTT 767s GTT 767s Processing line... 767s GTT 767s GTT 767s Processing line... 767s GTT 767s GTT 767s Processing line... 767s GTT 767s GTT 767s Processing line... 767s Processing line... 767s GGGT 767s GGGT 767s Processing line... 767s TGGGGG 767s TGGGGG 767s Processing line... 767s GGGT 767s GGGT 767s Processing line... 767s TGGGGG 767s TGGGGG 767s Processing line... 767s GGGT 767s GGGT 767s Processing line... 767s TGGGGG 767s TGGGGG 767s Processing line... 767s GGGGTA 767s GGGGTA 767s Processing line... 767s Processing line... 767s Processing line... 767s AGGGGCGATTAGTTGG 767s AGGGGCGATTAGTTGG 767s Processing line... 767s Processing line... 768s *** Run 37 of 100 768s /usr/bin/bowtie2 --cp-ival 1 -a --large-index --cp-min 12 --trim5 9 --score-min L,8.69472852957059,9.53244218428507 --ma 38.638502757192 --nofw -D 3 -R 3 -N 0 -L17 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s GGTTCGGGGGTGGCTGGGGGG 768s GGTTCGGGGGTGGCTGGGGGG 768s Processing line... 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s GGG 768s GGG 768s Processing line... 768s Processing line... 768s Processing line... 768s GGGTAGGGGCGATT 768s GGGTAGGGGCGATT 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s --- Summary --- 768s Read 1 reference strings 768s Checked 57 alignments, 0 edits 768s --------------- 768s PASSED 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.2 768s Introducing 18 SNPs, 0/0 ref/read gaps, and 2 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutating sequence Sim.pm.1 768s Introducing 9 SNPs, 1/2 ref/read gaps, and 1 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutated reference genome to subject genome 768s SNPs introduced: 27 768s Reference gaps introduced: 1 768s Read gaps introduced: 2 768s Rearrangements introduced: 3 768s Created read sampler 768s Sampling 176 reads 768s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 768s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 768s parsing sequence Sim.pm.1... 768s parsing sequence Sim.pm.2... 768s Parsed 76 reference bases 768s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 768s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 768s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '8' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 768s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '14' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 768s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '21' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 768s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '28' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 768s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '30' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 768s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '33' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 768s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '35' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 768s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '38' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 768s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '41' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 768s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '42' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 768s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '47' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 768s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '52' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 768s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '53' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 768s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '55' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 768s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '57' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 768s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '58' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 768s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '61' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 768s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '64' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 768s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '65' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 768s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '72' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 768s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '74' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 768s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '77' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 768s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '78' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 768s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '79' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 768s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '83' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 768s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '84' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 768s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '86' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 768s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '89' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 768s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '98' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 768s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '99' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 768s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '100' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 768s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '106' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 768s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '109' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 768s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '121' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 768s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '124' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 768s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '127' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 768s Warning: skipping read '131' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '131' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 768s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '132' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 768s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '133' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 768s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '135' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 768s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '137' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 768s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '138' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 768s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '145' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 768s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '152' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 768s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '153' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 768s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '154' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 768s Warning: skipping read '160' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '160' because it was < 2 characters long 768s Read 50 alignments... 768s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 768s Warning: skipping read '166' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '166' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 768s Warning: skipping read '167' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '167' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 768s Warning: skipping read '169' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '169' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 768s Warning: skipping read '172' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '172' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 768s Warning: skipping read '175' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '175' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 768s Warning: skipping read '176' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '176' because it was < 2 characters long 768s Read 100 alignments... 768s 176 reads; of these: 768s 176 (100.00%) were unpaired; of these: 768s 166 (94.32%) aligned 0 times 768s 6 (3.41%) aligned exactly 1 time 768s 4 (2.27%) aligned >1 times 768s 5.68% overall alignment rate 768s Read 150 alignments... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s TAGGGGCGATTAGTTGGAGT 768s TAGGGGCGATTAGTTGGAGT 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s TG 768s TG 768s Processing line... 768s TG 768s TG 768s Processing line... 768s TG 768s TG 768s Processing line... 768s TG 768s TG 768s Processing line... 768s TG 768s TG 768s Processing line... 768s TG 768s TG 768s Processing line... 768s TG 768s TG 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s GCTGGGGGGTAGGG 768s GCTGGGGGGTAGGG 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s CC 768s CC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s GGTAGGGGCGATTAGTTGG 768s GGTAGGGGCGATTAGTTGG 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s GC 768s GC 768s Processing line... 768s GC 768s GC 768s Processing line... 768s GC 768s GC 768s Processing line... 768s GC 768s GC 768s Processing line... 768s TCTCGGTTCGGGGGTGGCTGGGGGG 768s TCTCGGTTCGGGGGTGGCTGGGGGG 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s TGGG 768s TGGG 768s Processing line... 768s TGGG 768s TGGG 768s Processing line... 768s CCT 768s CCT 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s GC 768s GC 768s Processing line... 768s GC 768s GC 768s Processing line... 768s GC 768s GC 768s Processing line... 768s GC 768s GC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s --- Summary --- 768s Read 1 reference strings 768s Checked 23 alignments, 0 edits 768s --------------- 768s PASSED 768s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 768s /usr/bin/bowtie2 --cp-ival 1 -a --large-index --cp-min 12 --trim5 9 --score-min L,8.69472852957059,9.53244218428507 --ma 38.638502757192 --nofw -D 3 -R 3 -N 0 -L17 -f -p 3 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 768s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 768s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 768s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '8' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 768s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '14' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 768s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '21' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 768s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '28' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 768s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '30' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 768s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '33' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 768s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '35' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 768s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '38' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 768s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '41' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 768s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '42' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 768s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '47' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 768s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '52' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 768s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '53' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 768s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '55' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 768s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '57' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 768s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '58' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 768s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '61' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 768s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '64' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 768s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '65' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 768s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '72' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 768s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '74' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 768s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '77' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 768s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '78' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 768s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '79' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 768s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '83' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 768s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '84' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 768s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '86' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 768s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '89' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 768s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '98' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 768s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '99' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 768s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '100' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 768s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '106' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 768s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '109' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 768s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '121' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 768s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '124' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 768s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '127' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 768s Warning: skipping read '131' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '131' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 768s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '132' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 768s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '133' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 768s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '135' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 768s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '137' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 768s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '138' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 768s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '145' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 768s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '152' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 768s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '153' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 768s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '154' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 768s Warning: skipping read '160' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '160' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 768s Warning: skipping read '166' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '166' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 768s Warning: skipping read '167' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '167' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 768s Warning: skipping read '169' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '169' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 768s Warning: skipping read '172' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '172' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 768s Warning: skipping read '175' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '175' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 768s Warning: skipping read '176' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '176' because it was < 2 characters long 768s 176 reads; of these: 768s 176 (100.00%) were unpaired; of these: 768s 166 (94.32%) aligned 0 times 768s 6 (3.41%) aligned exactly 1 time 768s 4 (2.27%) aligned >1 times 768s 5.68% overall alignment rate 768s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.2 768s Introducing 16 SNPs, 1/3 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutating sequence Sim.pm.1 768s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutated reference genome to subject genome 768s SNPs introduced: 17 768s Reference gaps introduced: 1 768s Read gaps introduced: 4 768s Rearrangements introduced: 0 768s Created read sampler 768s Sampling 133 reads 768s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 768s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 768s parsing sequence Sim.pm.1... 768s parsing sequence Sim.pm.2... 768s Parsed 76 reference bases 768s *** Run 38 of 100 768s /usr/bin/bowtie2 --local --cp-ival 2 --trim3 6 -N 0 -L29 --mp 9.9773640116099,8.33594319110512 --cp-min 4 --np 3 --large-index --mm --score-min L,2.7399702169455,7.94884235349093 --gbar 2 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 768s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 768s Read 50 alignments... 768s Read 100 alignments... 768s 133 reads; of these: 768s 133 (100.00%) were unpaired; of these: 768s 133 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 0.00% overall alignment rate 768s Processing line... 768s Processing line... 768s Processing line... 768s /usr/bin/bowtie2 --local --cp-ival 2 --trim3 6 -N 0 -L29 --mp 9.9773640116099,8.33594319110512 --cp-min 4 --np 3 --large-index --mm --score-min L,2.7399702169455,7.94884235349093 --gbar 2 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s --- Summary --- 768s Read 1 reference strings 768s Checked 0 alignments, 0 edits 768s --------------- 768s PASSED 768s ALSO checking that bowtie2 and bowtie2-align match up 768s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 768s Warning: skipping read 'R_1_1_1_125_125_1/1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 768s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 768s 133 reads; of these: 768s 133 (100.00%) were unpaired; of these: 768s 133 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 0.00% overall alignment rate 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.2 768s Introducing 1 SNPs, 2/0 ref/read gaps, and 1 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutating sequence Sim.pm.1 768s Introducing 0 SNPs, 3/0 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutated reference genome to subject genome 768s SNPs introduced: 1 768s Reference gaps introduced: 5 768s Read gaps introduced: 0 768s Rearrangements introduced: 1 768s Created read sampler 768s Sampling 273 reads 768s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 768s *** Run 39 of 100 768s /usr/bin/bowtie2 --trim3 3 --nofw -N 0 -L16 --local --cp-ival 1 -M 5 --trim5 6 --rdg 29.3030297149706 --score-min L,1.75275111849599,6.00499332250302 --np 8 --cp-min 3 --large-index -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 768s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 768s parsing sequence Sim.pm.1... 768s parsing sequence Sim.pm.2... 768s Parsed 76 reference bases 768s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 768s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '5' because it was < 2 characters long 768s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '7' because it was < 2 characters long 768s Warning: skipping mate #1 of read '10' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '10' because it was < 2 characters long 768s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '11' because it was < 2 characters long 768s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '16' because it was < 2 characters long 768s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '30' because it was < 2 characters long 768s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '34' because it was < 2 characters long 768s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '36' because it was < 2 characters long 768s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '38' because it was < 2 characters long 768s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '44' because it was < 2 characters long 768s Warning: skipping mate #1 of read '48' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '48' because it was < 2 characters long 768s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '49' because it was < 2 characters long 768s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '57' because it was < 2 characters long 768s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '58' because it was < 2 characters long 768s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '63' because it was < 2 characters long 768s Read 50 alignments... 768s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #2 of read '66' because it was < 2 characters long 768s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '75' because it was < 2 characters long 768s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '80' because it was < 2 characters long 768s Read 100 alignments... 768s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '84' because it was < 2 characters long 768s Warning: skipping mate #1 of read '91' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '91' because it was < 2 characters long 768s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '98' because it was < 2 characters long 768s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '99' because it was < 2 characters long 768s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '100' because it was < 2 characters long 768s Warning: skipping mate #2 of read '103' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #2 of read '103' because it was < 2 characters long 768s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '107' because it was < 2 characters long 768s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '110' because it was < 2 characters long 768s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '117' because it was < 2 characters long 768s Warning: skipping mate #1 of read '121' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '121' because it was < 2 characters long 768s Warning: skipping mate #1 of read '123' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '123' because it was < 2 characters long 768s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '126' because it was < 2 characters long 768s Warning: skipping mate #1 of read '130' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '130' because it was < 2 characters long 768s Warning: skipping mate #1 of read '135' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '135' because it was < 2 characters long 768s Warning: skipping mate #1 of read '137' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '137' because it was < 2 characters long 768s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '138' because it was < 2 characters long 768s Warning: skipping mate #1 of read '141' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '141' because it was < 2 characters long 768s Warning: skipping mate #1 of read '153' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '153' because it was < 2 characters long 768s Warning: skipping mate #1 of read '155' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '155' because it was < 2 characters long 768s Warning: skipping mate #1 of read '156' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #2 of read '156' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '156' because it was < 2 characters long 768s Warning: skipping mate #2 of read '156' because it was < 2 characters long 768s Read 150 alignments... 768s Read 200 alignments... 768s Warning: skipping read '161' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '161' because it was < 2 characters long 768s Warning: skipping mate #1 of read '169' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '169' because it was < 2 characters long 768s Read 250 alignments... 768s Read 300 alignments... 768s Warning: skipping mate #2 of read '180' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #2 of read '180' because it was < 2 characters long 768s Warning: skipping mate #1 of read '184' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '184' because it was < 2 characters long 768s Warning: skipping read '188' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '188' because it was < 2 characters long 768s Warning: skipping mate #1 of read '192' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '192' because it was < 2 characters long 768s Warning: skipping read '204' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '204' because it was < 2 characters long 768s Warning: skipping mate #1 of read '206' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '206' because it was < 2 characters long 768s Warning: skipping mate #1 of read '209' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '209' because it was < 2 characters long 768s Warning: skipping mate #1 of read '218' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '218' because it was < 2 characters long 768s Warning: skipping mate #1 of read '221' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '221' because it was < 2 characters long 768s Warning: skipping mate #1 of read '222' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '222' because it was < 2 characters long 768s Warning: skipping mate #1 of read '227' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '227' because it was < 2 characters long 768s Warning: skipping mate #1 of read '231' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '231' because it was < 2 characters long 768s Warning: skipping mate #1 of read '233' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '233' because it was < 2 characters long 768s Warning: skipping read '235' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '235' because it was < 2 characters long 768s Warning: skipping read '236' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '236' because it was < 2 characters long 768s Warning: skipping read '238' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '238' because it was < 2 characters long 768s Warning: skipping mate #1 of read '241' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '241' because it was < 2 characters long 768s Warning: skipping read '246' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '246' because it was < 2 characters long 768s Warning: skipping read '248' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '248' because it was < 2 characters long 768s Warning: skipping read '252' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '252' because it was < 2 characters long 768s Warning: skipping mate #1 of read '253' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '253' because it was < 2 characters long 768s Warning: skipping read '254' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '254' because it was < 2 characters long 768s Warning: skipping mate #1 of read '257' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '257' because it was < 2 characters long 768s Warning: skipping mate #1 of read '261' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '261' because it was < 2 characters long 768s Read 350 alignments... 768s 273 reads; of these: 768s 216 (79.12%) were paired; of these: 768s 216 (100.00%) aligned concordantly 0 times 768s 0 (0.00%) aligned concordantly exactly 1 time 768s 0 (0.00%) aligned concordantly >1 times 768s ---- 768s 216 pairs aligned concordantly 0 times; of these: 768s 0 (0.00%) aligned discordantly 1 time 768s ---- 768s 216 pairs aligned 0 times concordantly or discordantly; of these: 768s 432 mates make up the pairs; of these: 768s 432 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 57 (20.88%) were unpaired; of these: 768s 57 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 0.00% overall alignment rate 768s Read 400 alignments... 768s Read 450 alignments... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing 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line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s --- Summary --- 768s Read 1 reference strings 768s Checked 0 alignments, 0 edits 768s --------------- 768s PASSED 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.1 768s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutating sequence Sim.pm.2 768s Introducing 2 SNPs, 0/3 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutated reference genome to subject genome 768s SNPs introduced: 5 768s Reference gaps introduced: 0 768s Read gaps introduced: 3 768s Rearrangements introduced: 0 768s Created read sampler 768s Sampling 12 reads 768s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 768s *** Run 40 of 100 768s /usr/bin/bowtie2 --gbar 1 -D 43 --score-min L,1.08157220712567,6.8203773599733 --mm --cp-min 5 --large-index --mp 9.69869665773083,3.91482699697851 --trim3 4 --nofw --rfg 5.52605671701712,10.0824548080604 --trim5 8 -a --cp-ival 1 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 768s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 768s parsing sequence Sim.pm.1... 768s parsing sequence Sim.pm.2... 768s Parsed 76 reference bases 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 769s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 769s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 769s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 769s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 769s /usr/bin/bowtie2 --gbar 1 -D 43 --score-min L,1.08157220712567,6.8203773599733 --mm --cp-min 5 --large-index --mp 9.69869665773083,3.91482699697851 --trim3 4 --nofw --rfg 5.52605671701712,10.0824548080604 --trim5 8 -a --cp-ival 1 --qseq -p 3 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 769s 12 reads; of these: 769s 11 (91.67%) were paired; of these: 769s 11 (100.00%) aligned concordantly 0 times 769s 0 (0.00%) aligned concordantly exactly 1 time 769s 0 (0.00%) aligned concordantly >1 times 769s ---- 769s 11 pairs aligned concordantly 0 times; of these: 769s 0 (0.00%) aligned discordantly 1 time 769s ---- 769s 11 pairs aligned 0 times concordantly or discordantly; of these: 769s 22 mates make up the pairs; of these: 769s 20 (90.91%) aligned 0 times 769s 2 (9.09%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 1 (8.33%) were unpaired; of these: 769s 1 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 8.70% overall alignment rate 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GTGGCTGGGG 769s GTGGCTGGGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GGGGTGGC 769s GGGGTGGC 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s --- Summary --- 769s Read 1 reference strings 769s Checked 2 alignments, 0 edits 769s --------------- 769s PASSED 769s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 769s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 769s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 769s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 769s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 769s 12 reads; of these: 769s 11 (91.67%) were paired; of these: 769s 11 (100.00%) aligned concordantly 0 times 769s 0 (0.00%) aligned concordantly exactly 1 time 769s 0 (0.00%) aligned concordantly >1 times 769s ---- 769s 11 pairs aligned concordantly 0 times; of these: 769s 0 (0.00%) aligned discordantly 1 time 769s ---- 769s 11 pairs aligned 0 times concordantly or discordantly; of these: 769s 22 mates make up the pairs; of these: 769s 20 (90.91%) aligned 0 times 769s 2 (9.09%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 1 (8.33%) were unpaired; of these: 769s 1 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 8.70% overall alignment rate 769s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 769s Flattened IUPAC characters 769s Mutating sequence Sim.pm.1 769s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutating sequence Sim.pm.2 769s Introducing 1 SNPs, 0/1 ref/read gaps, and 3 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutated reference genome to subject genome 769s SNPs introduced: 2 769s Reference gaps introduced: 0 769s Read gaps introduced: 1 769s Rearrangements introduced: 4 769s Created read sampler 769s Sampling 161 reads 769s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 769s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 769s parsing sequence Sim.pm.1... 769s *** Run 41 of 100 769s /usr/bin/bowtie2 --np 9 --cp-min 10 --large-index --n-ceil 0.847442572718775,0.0398395100544944 --cp-ival 2 --score-min L,2.38894226730805,9.44518285982336 --mp 9.9121766446787,3.57167893349785 -k 13 -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw 769s parsing sequence Sim.pm.2... 769s Parsed 76 reference bases 769s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 769s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '10' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 769s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '13' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 769s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '41' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 769s Warning: skipping read '67' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '67' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 769s Warning: skipping read '127' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '127' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 769s Read 50 alignments... 769s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 769s Read 100 alignments... 769s 161 reads; of these: 769s 161 (100.00%) were unpaired; of these: 769s 141 (87.58%) aligned 0 times 769s 12 (7.45%) aligned exactly 1 time 769s 8 (4.97%) aligned >1 times 769s 12.42% overall alignment rate 769s Read 150 alignments... 769s Read 200 alignments... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s ACCTGGGGG 769s ACCTGGGGG 769s Processing line... 769s Processing line... 769s ACCTGGGGG 769s ACCTGGGGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CT 769s CT 769s Processing line... 769s AG 769s AG 769s Processing line... 769s CT 769s CT 769s Processing line... 769s CT 769s CT 769s Processing line... 769s AG 769s AG 769s Processing line... 769s CT 769s CT 769s Processing line... 769s AG 769s AG 769s Processing line... 769s CT 769s CT 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGTT 769s CGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGTT 769s Processing line... 769s Processing line... 769s Processing line... 769s GGGT 769s GGGT 769s Processing line... 769s GGGT 769s GGGT 769s Processing line... 769s GGGT 769s GGGT 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GGGG 769s GGGG 769s Processing line... 769s GGGG 769s GGGG 769s Processing line... 769s GGGG 769s GGGG 769s Processing line... 769s GGGG 769s GGGG 769s Processing line... 769s GGGG 769s GGGG 769s Processing line... 769s GGGG 769s GGGG 769s Processing line... 769s GGGG 769s GGGG 769s Processing line... 769s GGGG 769s GGGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CGATTAGTTG 769s CGATTAGTTG 769s Processing line... 769s GCTGGGGGGTAGGGGCG 769s GCTGGGGGGTAGGGGCG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CT 769s CT 769s Processing line... 769s CT 769s CT 769s Processing line... 769s CT 769s CT 769s Processing line... 769s AG 769s AG 769s Processing line... 769s AG 769s AG 769s Processing line... 769s CT 769s CT 769s Processing line... 769s CT 769s CT 769s Processing line... 769s AG 769s AG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s TGGGGGGTAGGGG 769s TGGGGGGTAGGGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CTGGGGGGTAGGGGCGATTAGTTGGAG 769s CTGGGGGGTAGGGGCGATTAGTTGGAG 769s Processing line... 769s TTGGAGTT 769s TTGGAGTT 769s Processing line... 769s TCGGGGGTGGCTGGGGGGTA 769s TCGGGGGTGGCTGGGGGGTA 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s TTGGAGTT 769s TTGGAGTT 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s TC 769s TC 769s Processing line... 769s TC 769s TC 769s Processing line... 769s GA 769s GA 769s Processing line... 769s TC 769s TC 769s Processing line... 769s TC 769s TC 769s Processing line... 769s GA 769s GA 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s GGG 769s GGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s AG 769s AG 769s Processing line... 769s CT 769s CT 769s Processing line... 769s CT 769s CT 769s Processing line... 769s CT 769s CT 769s Processing line... 769s CT 769s CT 769s Processing line... 769s CT 769s CT 769s Processing line... 769s AG 769s AG 769s Processing line... 769s AG 769s AG 769s Processing line... 769s ACCTGGG 769s ACCTGGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s Processing line... 769s Processing line... 769s GGTAGGGG 769s GGTAGGGG 769s Processing line... 769s /usr/bin/bowtie2 --np 9 --cp-min 10 --large-index --n-ceil 0.847442572718775,0.0398395100544944 --cp-ival 2 --score-min L,2.38894226730805,9.44518285982336 --mp 9.9121766446787,3.57167893349785 -k 13 -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 769s Processing line... 769s Processing line... 769s Processing line... 769s --- Summary --- 769s Read 1 reference strings 769s Checked 79 alignments, 0 edits 769s --------------- 769s PASSED 769s ALSO checking that bowtie2 and bowtie2-align match up 769s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 769s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '10' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 769s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '13' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 769s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '41' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 769s Warning: skipping read '67' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '67' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 769s Warning: skipping read '127' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '127' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 769s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 769s 161 reads; of these: 769s 161 (100.00%) were unpaired; of these: 769s 141 (87.58%) aligned 0 times 769s 12 (7.45%) aligned exactly 1 time 769s 8 (4.97%) aligned >1 times 769s 12.42% overall alignment rate 769s /usr/bin/bowtie2 --np 9 --cp-min 10 --large-index --n-ceil 0.847442572718775,0.0398395100544944 --cp-ival 2 --score-min L,2.38894226730805,9.44518285982336 --mp 9.9121766446787,3.57167893349785 -k 13 -r -p 3 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 769s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 769s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 769s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '10' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 769s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '13' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 769s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '41' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 769s Warning: skipping read '67' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '67' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 769s Warning: skipping read '127' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '127' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 769s 161 reads; of these: 769s 161 (100.00%) were unpaired; of these: 769s 141 (87.58%) aligned 0 times 769s 12 (7.45%) aligned exactly 1 time 769s 8 (4.97%) aligned >1 times 769s 12.42% overall alignment rate 769s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 769s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 769s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 769s Flattened IUPAC characters 769s Mutating sequence Sim.pm.1 769s Introducing 9 SNPs, 0/1 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutating sequence Sim.pm.2 769s Introducing 9 SNPs, 2/0 ref/read gaps, and 1 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutated reference genome to subject genome 769s SNPs introduced: 18 769s Reference gaps introduced: 2 769s Read gaps introduced: 1 769s Rearrangements introduced: 1 769s Created read sampler 769s Sampling 84 reads 769s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 769s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 769s parsing sequence Sim.pm.1... 769s parsing sequence Sim.pm.2... 769s Parsed 76 reference bases 769s *** Run 42 of 100 769s /usr/bin/bowtie2 --cp-ival 1 --local --trim5 5 --large-index -a --np 1 --cp-min 5 --rfg 30.142442259522,18.5261605329456 --score-min L,3.43694623007459,6.67281097322187 --trim3 3 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 769s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (1) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 769s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 769s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 769s 84 reads; of these: 769s 84 (100.00%) were unpaired; of these: 769s 84 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s Read 50 alignments... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s --- Summary --- 769s Read 1 reference strings 769s Checked 0 alignments, 0 edits 769s --------------- 769s PASSED 769s Flattened IUPAC characters 769s Mutating sequence Sim.pm.1 769s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutating sequence Sim.pm.2 769s Introducing 12 SNPs, 1/0 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutated reference genome to subject genome 769s SNPs introduced: 16 769s Reference gaps introduced: 1 769s Read gaps introduced: 0 769s Rearrangements introduced: 1 769s Created read sampler 769s Sampling 59 reads 769s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 769s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 769s parsing sequence Sim.pm.1... 769s parsing sequence Sim.pm.2... 769s Parsed 76 reference bases 769s *** Run 43 of 100 769s /usr/bin/bowtie2 --cp-min 9 --np 4 --score-min L,5.74756138284817,7.02597173173334 --large-index --cp-ival 2 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 769s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 769s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '15' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 769s 59 reads; of these: 769s 59 (100.00%) were unpaired; of these: 769s 49 (83.05%) aligned 0 times 769s 9 (15.25%) aligned exactly 1 time 769s 1 (1.69%) aligned >1 times 769s 16.95% overall alignment rate 769s Read 50 alignments... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CGGGGGTGGCTGGG 769s CGGGGGTGGCTGGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GCG 769s GCG 769s Processing line... 769s CTCGG 769s CTCGG 769s Processing line... 769s TAGTTGG 769s TAGTTGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CTGGGGGGTAGGGG 769s CTGGGGGGTAGGGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GGA 769s GGA 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GGTGG 769s GGTGG 769s Processing line... 769s TTCGGGG 769s TTCGGGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GATTAGTTGGAG 769s GATTAGTTGGAG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GGGT 769s GGGT 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s --- Summary --- 769s Read 1 reference strings 769s Checked 10 alignments, 0 edits 769s --------------- 769s PASSED 769s ALSO checking that bowtie2 and bowtie2-align match up 769s /usr/bin/bowtie2 --cp-min 9 --np 4 --score-min L,5.74756138284817,7.02597173173334 --large-index --cp-ival 2 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 769s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 769s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '15' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 769s 59 reads; of these: 769s 59 (100.00%) were unpaired; of these: 769s 49 (83.05%) aligned 0 times 769s 9 (15.25%) aligned exactly 1 time 769s 1 (1.69%) aligned >1 times 769s 16.95% overall alignment rate 769s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 769s /usr/bin/bowtie2 --cp-min 9 --np 4 --score-min L,5.74756138284817,7.02597173173334 --large-index --cp-ival 2 -f -p 3 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 769s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 769s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 769s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '15' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 769s 59 reads; of these: 769s 59 (100.00%) were unpaired; of these: 769s 49 (83.05%) aligned 0 times 769s 9 (15.25%) aligned exactly 1 time 769s 1 (1.69%) aligned >1 times 769s 16.95% overall alignment rate 769s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 769s Flattened IUPAC characters 769s Mutating sequence Sim.pm.2 769s Introducing 18 SNPs, 0/2 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutating sequence Sim.pm.1 769s Introducing 9 SNPs, 0/1 ref/read gaps, and 2 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutated reference genome to subject genome 769s SNPs introduced: 27 769s Reference gaps introduced: 0 769s Read gaps introduced: 3 769s Rearrangements introduced: 2 769s Created read sampler 769s Sampling 161 reads 769s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 769s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 769s *** Run 44 of 100 769s /usr/bin/bowtie2 --large-index --np 9 --cp-min 6 --score-min L,8.99819905909101,7.35161712760453 -R 1 --rdg 32.7976128844531,6.90129482308871 --mm -a --n-ceil 0.365254223368414,0.280888181121785 --cp-ival 1 -i S,1.89394174003277,5.88087707193315 -q -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq 769s parsing sequence Sim.pm.1... 769s parsing sequence Sim.pm.2... 769s Parsed 76 reference bases 769s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 769s Warning: skipping read '84' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '84' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 769s Read 50 alignments... 769s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 769s Warning: skipping read '161' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '161' because it was < 2 characters long 769s Read 100 alignments... 769s 161 reads; of these: 769s 161 (100.00%) were unpaired; of these: 769s 141 (87.58%) aligned 0 times 769s 7 (4.35%) aligned exactly 1 time 769s 13 (8.07%) aligned >1 times 769s 12.42% overall alignment rate 769s Read 150 alignments... 769s Read 200 alignments... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GTA 769s GTA 769s Processing line... 769s TAC 769s TAC 769s Processing line... 769s Processing line... 769s TGGGG 769s TGGGG 769s Processing line... 769s TGGGG 769s TGGGG 769s Processing line... 769s AGTTGG 769s AGTTGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GCGATTAGTTGGAG 769s GCGATTAGTTGGAG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GGCTGGGGGGTAGGGGCGATTAG 769s GGCTGGGGGGTAGGGGCGATTAG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s TA 769s TA 769s Processing line... 769s TA 769s TA 769s Processing line... 769s TA 769s TA 769s Processing line... 769s TA 769s TA 769s Processing line... 769s TA 769s TA 769s Processing line... 769s TA 769s TA 769s Processing line... 769s Processing line... 769s TGGG 769s TGGG 769s Processing line... 769s TGGG 769s TGGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GCT 769s GCT 769s Processing line... 769s GCT 769s GCT 769s Processing line... 769s TGGG 769s TGGG 769s Processing line... 769s TGGG 769s TGGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GT 769s GT 769s Processing line... 769s GT 769s GT 769s Processing line... 769s GT 769s GT 769s Processing line... 769s GT 769s GT 769s Processing line... 769s GT 769s GT 769s Processing line... 769s GT 769s GT 769s Processing line... 769s AC 769s AC 769s Processing line... 769s GT 769s GT 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CGG 769s CGG 769s Processing line... 769s CGG 769s CGG 769s Processing line... 769s Processing line... 769s Processing line... 769s GTGC 769s GTGC 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GGTA 769s GGTA 769s Processing line... 769s TACC 769s TACC 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GCGATTAGTTGGAG 769s GCGATTAGTTGGAG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GAGTT 769s GAGTT 769s Processing line... 769s AT 769s AT 769s Processing line... 769s AT 769s AT 769s Processing line... 769s TC 769s TC 769s Processing line... 769s TC 769s TC 769s Processing line... 769s GA 769s GA 769s Processing line... 769s TC 769s TC 769s Processing line... 769s TC 769s TC 769s Processing line... 769s GA 769s GA 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s CC 769s CC 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s GG 769s GG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CGG 769s CGG 769s Processing line... 769s CGG 769s CGG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GGCTGGGGGGTAGGGGCGAT 769s GGCTGGGGGGTAGGGGCGAT 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s --- Summary --- 769s Read 1 reference strings 769s Checked 69 alignments, 0 edits 769s --------------- 769s PASSED 769s ALSO checking that bowtie2 and bowtie2-align match up 769s /usr/bin/bowtie2 --large-index --np 9 --cp-min 6 --score-min L,8.99819905909101,7.35161712760453 -R 1 --rdg 32.7976128844531,6.90129482308871 --mm -a --n-ceil 0.365254223368414,0.280888181121785 --cp-ival 1 -i S,1.89394174003277,5.88087707193315 -q -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 770s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 770s Warning: skipping read '84' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '84' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 770s Warning: skipping read '161' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '161' because it was < 2 characters long 770s 161 reads; of these: 770s 161 (100.00%) were unpaired; of these: 770s 141 (87.58%) aligned 0 times 770s 7 (4.35%) aligned exactly 1 time 770s 13 (8.07%) aligned >1 times 770s 12.42% overall alignment rate 770s Flattened IUPAC characters 770s Mutating sequence Sim.pm.2 770s Introducing 19 SNPs, 2/1 ref/read gaps, and 0 rearrangements 770s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutating sequence Sim.pm.1 770s Introducing 10 SNPs, 6/1 ref/read gaps, and 1 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutated reference genome to subject genome 770s SNPs introduced: 29 770s Reference gaps introduced: 8 770s Read gaps introduced: 2 770s Rearrangements introduced: 1 770s Created read sampler 770s Sampling 58 reads 770s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 770s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 770s parsing sequence Sim.pm.1... 770s parsing sequence Sim.pm.2... 770s *** Run 45 of 100 770s /usr/bin/bowtie2 -N 0 -L14 --gbar 2 -k 2 --trim3 6 --score-min L,5.40923423403171,7.40280806098072 --rdg 5.25648540342285 --cp-min 2 --large-index --cp-ival 2 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 770s Parsed 76 reference bases 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 770s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '3' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 770s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '5' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 770s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '10' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 770s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '13' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 770s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '19' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 770s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '24' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 770s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '29' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 770s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '37' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 770s Warning: skipping mate #1 of read '40' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '40' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 770s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '45' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 770s 58 reads; of these: 770s 53 (91.38%) were paired; of these: 770s 53 (100.00%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 0 (0.00%) aligned concordantly >1 times 770s ---- 770s 53 pairs aligned concordantly 0 times; of these: 770s 0 (0.00%) aligned discordantly 1 time 770s ---- 770s 53 pairs aligned 0 times concordantly or discordantly; of these: 770s 106 mates make up the pairs; of these: 770s 97 (91.51%) aligned 0 times 770s 6 (5.66%) aligned exactly 1 time 770s 3 (2.83%) aligned >1 times 770s 5 (8.62%) were unpaired; of these: 770s 5 (100.00%) aligned 0 times 770s 0 (0.00%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 8.11% overall alignment rate 770s Read 50 alignments... 770s Read 100 alignments... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GGCT 770s GGCT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GTTGG 770s GTTGG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CGGTTCGGGGGTGGCTGGGGGGTAG 770s CGGTTCGGGGGTGGCTGGGGGGTAG 770s Processing line... 770s Processing line... 770s TC 770s TC 770s Processing line... 770s TC 770s TC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GT 770s GT 770s Processing line... 770s GT 770s GT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TCGGTTCGGGGGTGGCTG 770s TCGGTTCGGGGGTGGCTG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GGG 770s GGG 770s Processing line... 770s GGG 770s GGG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CGGTTCGGGGGTGGCTGG 770s CGGTTCGGGGGTGGCTGG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AGTTGGAGTTCT 770s AGTTGGAGTTCT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s --- Summary --- 770s Read 1 reference strings 770s Checked 12 alignments, 0 edits 770s --------------- 770s PASSED 770s Flattened IUPAC characters 770s Mutating sequence Sim.pm.1 770s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutating sequence Sim.pm.2 770s Introducing 1 SNPs, 0/2 ref/read gaps, and 1 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s *** Run 46 of 100 770s /usr/bin/bowtie2 --cp-ival 3 --large-index --cp-min 5 --trim5 5 --norc --rdg 27.1750112627055 --mm --score-min L,4.06509213034661,3.84764942249758 --trim3 6 -k 2 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 770s Mutated reference genome to subject genome 770s SNPs introduced: 5 770s Reference gaps introduced: 0 770s Read gaps introduced: 2 770s Rearrangements introduced: 1 770s Created read sampler 770s Sampling 100 reads 770s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 770s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 770s parsing sequence Sim.pm.1... 770s parsing sequence Sim.pm.2... 770s Parsed 76 reference bases 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 770s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 770s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 770s Warning: skipping mate #2 of read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 770s Read 50 alignments... 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 770s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 770s Warning: skipping mate #2 of read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 770s 100 reads; of these: 770s 84 (84.00%) were paired; of these: 770s 83 (98.81%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 1 (1.19%) aligned concordantly >1 times 770s ---- 770s 83 pairs aligned concordantly 0 times; of these: 770s 0 (0.00%) aligned discordantly 1 time 770s ---- 770s 83 pairs aligned 0 times concordantly or discordantly; of these: 770s 166 mates make up the pairs; of these: 770s 152 (91.57%) aligned 0 times 770s 11 (6.63%) aligned exactly 1 time 770s 3 (1.81%) aligned >1 times 770s 16 (16.00%) were unpaired; of these: 770s 14 (87.50%) aligned 0 times 770s 2 (12.50%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 9.78% overall alignment rate 770s Read 100 alignments... 770s Read 150 alignments... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GTGC 770s GTGC 770s Processing line... 770s GC 770s GC 770s Processing line... 770s GG 770s GG 770s Processing line... 770s GC 770s GC 770s Processing line... 770s GG 770s GG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TAGGGGCGATTA 770s TAGGGGCGATTA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AGGG 770s AGGG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GGCTGG 770s GGCTGG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GGTA 770s GGTA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GGGGTAGGGGCGA 770s GGGGTAGGGGCGA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AC 770s AC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TAGTT 770s TAGTT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TGC 770s TGC 770s Processing line... 770s TGC 770s TGC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CT 770s CT 770s Processing line... 770s CT 770s CT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CC 770s CC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GGGGTAGGGGCGATTAGTTGGAG 770s GGGGTAGGGGCGATTAGTTGGAG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CGGG 770s CGGG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CC 770s CC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TTG 770s TTG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GC 770s GC 770s Processing line... 770s GC 770s GC 770s Processing line... 770s --- Summary --- 770s Read 1 reference strings 770s Checked 23 alignments, 0 edits 770s --------------- 770s PASSED 770s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 770s /usr/bin/bowtie2 --cp-ival 3 --large-index --cp-min 5 --trim5 5 --norc --rdg 27.1750112627055 --mm --score-min L,4.06509213034661,3.84764942249758 --trim3 6 -k 2 --qseq -p 4 -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 770s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 770s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 770s Warning: skipping mate #2 of read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 770s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 770s Warning: skipping mate #2 of read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 770s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 770s 100 reads; of these: 770s 84 (84.00%) were paired; of these: 770s 83 (98.81%) aligned concordantly 0 times 770s 0sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 770s (0.00%) aligned concordantly exactly 1 time 770s 1 (1.19%) aligned concordantly >1 times 770s ---- 770s 83 pairs aligned concordantly 0 times; of these: 770s 0 (0.00%) aligned discordantly 1 time 770s ---- 770s 83 pairs aligned 0 times concordantly or discordantly; of these: 770s 166 mates make up the pairs; of these: 770s 152 (91.57%) aligned 0 times 770s 11 (6.63%) aligned exactly 1 time 770s 3 (1.81%) aligned >1 times 770s 16 (16.00%) were unpaired; of these: 770s 14 (87.50%) aligned 0 times 770s 2 (12.50%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 9.78% overall alignment rate 770s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 770s Flattened IUPAC characters 770s Mutating sequence Sim.pm.1 770s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutating sequence Sim.pm.2 770s Introducing 21 SNPs, 0/0 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutated reference genome to subject genome 770s SNPs introduced: 23 770s Reference gaps introduced: 1 770s Read gaps introduced: 0 770s Rearrangements introduced: 0 770s Created read sampler 770s Sampling 36 reads 770s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 770s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 770s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 770s *** Run 47 of 100 770s /usr/bin/bowtie2 --rdg 13.4134294107284,1.3055619755633 --score-min L,3.35200090190399,2.53311399990445 --gbar 2 --local --cp-ival 4 --large-index -a --np 1 --cp-min 8 --norc --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 770s parsing sequence Sim.pm.1... 770s parsing sequence Sim.pm.2... 770s Parsed 76 reference bases 770s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 770s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 770s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 770s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 770s 36 reads; of these: 770s 36 (100.00%) were unpaired; of these: 770s 36 (100.00%) aligned 0 times 770s 0 (0.00%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 0.00% overall alignment rate 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s --- Summary --- 770s Read 1 reference strings 770s Checked 0 alignments, 0 edits 770s --------------- 770s PASSED 770s Flattened IUPAC characters 770s Mutating sequence Sim.pm.1 770s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutating sequence Sim.pm.2 770s Introducing 1 SNPs, 3/3 ref/read gaps, and 1 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutated reference genome to subject genome 770s SNPs introduced: 5 770s Reference gaps introduced: 4 770s Read gaps introduced: 3 770s Rearrangements introduced: 1 770s Created read sampler 770s Sampling 53 reads 770s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 770s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 770s parsing sequence Sim.pm.1... 770s parsing sequence Sim.pm.2... 770s Parsed 76 reference bases 770s *** Run 48 of 100 770s /usr/bin/bowtie2 --large-index --np 6 --cp-min 5 --score-min L,3.27140662403291,9.02013544771425 --ma 20.2051924757852 -k 3 --rdg 4.93944471695125 --mm --n-ceil 0.18116542505988,0.083036926602078 --cp-ival 3 -N 0 -L24 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 770s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 770s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '6' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 770s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '13' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 770s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '43' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 770s Read 50 alignments... 770s 53 reads; of these: 770s 53 (100.00%) were paired; of these: 770s 53 (100.00%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 0 (0.00%) aligned concordantly >1 times 770s ---- 770s 53 pairs aligned concordantly 0 times; of these: 770s 1 (1.89%) aligned discordantly 1 time 770s ---- 770s 52 pairs align*** Run 49 of 100 770s /usr/bin/bowtie2 --cp-min 6 --large-index --score-min L,5.20863702741179,3.66596797183495 --gbar 4 --rdg 14.615233304582 --mm -a --trim5 5 --local --cp-ival 1 -N 0 -L18 -i L,0.0520904336253586,2.80361841167676 --mp 6.751296322262,6.15510171846657 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 770s ed 0 times concordantly or discordantly; of these: 770s 104 mates make up the pairs; of these: 770s 93 (89.42%) aligned 0 times 770s 7 (6.73%) aligned exactly 1 time 770s 4 (3.85%) aligned >1 times 770s 12.26% overall alignment rate 770s Read 100 alignments... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CTGGGGGGTAGGGGCG 770s CTGGGGGGTAGGGGCG 770s Processing line... 770s GGCGATTAGTTGGAGTTCT 770s GGCGATTAGTTGGAGTTCT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TGCTC 770s TGCTC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TG 770s TG 770s Processing line... 770s TG 770s TG 770s Processing line... 770s TG 770s TG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TTAGTTGGAGT 770s TTAGTTGGAGT 770s Processing line... 770s Processing line... 770s GC 770s GC 770s Processing line... 770s GC 770s GC 770s Processing line... 770s GC 770s GC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GTGC 770s GTGC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GGAG 770s GGAG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GGCGATT 770s GGCGATT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TAGGGGCGA 770s TAGGGGCGA 770s Processing line... 770s Processing line... 770s GGGGTGGCTGG 770s GGGGTGGCTGG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GGG 770s GGG 770s Processing line... 770s GGG 770s GGG 770s Processing line... 770s GGG 770s GGG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GGC 770s GGC 770s Processing line... 770s GGC 770s GGC 770s Processing line... 770s --- Summary --- 770s Read 1 reference strings 770s Checked 20 alignments, 0 edits 770s --------------- 770s PASSED 770s Flattened IUPAC characters 770s Mutating sequence Sim.pm.1 770s Introducing 13 SNPs, 0/0 ref/read gaps, and 2 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutating sequence Sim.pm.2 770s Introducing 0 SNPs, 0/3 ref/read gaps, and 1 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutated reference genome to subject genome 770s SNPs introduced: 13 770s Reference gaps introduced: 0 770s Read gaps introduced: 3 770s Rearrangements introduced: 3 770s Created read sampler 770s Sampling 117 reads 770s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 770s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 770s parsing sequence Sim.pm.1... 770s parsing sequence Sim.pm.2... 770s Parsed 76 reference bases 771s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 771s 117 reads; of these: 771s 117 (100.00%) were unpaired; of these: 771s 117 (100.00%) aligned 0 times 771s 0 (0.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 0.00% overall alignment rate 771s Read 50 alignments... 771s Read 100 alignments... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s --- Summary --- 771s Read 1 reference strings 771s Checked 0 alignments, 0 edits 771s --------------- 771s PASSED 771s Flattened IUPAC characters 771s Mutating sequence Sim.pm.1 771s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutating sequence Sim.pm.2 771s Introducing 19 SNPs, 2/1 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutated reference genome to subject genome 771s SNPs introduced: 29 771s Reference gaps introduced: 2 771s Read gaps introduced: 1 771s Rearrangements introduced: 0 771s Created read sampler 771s Sampling 110 reads 771s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 771s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 771s parsing sequence Sim.pm.1... 771s parsing sequence Sim.pm.2... 771s *** Run 50 of 100 771s /usr/bin/bowtie2 --trim5 5 --local --cp-ival 2 --trim3 6 --cp-min 4 --np 1 --large-index --score-min L,9.15660414812684,9.17943970125745 -R 3 -D 30 --rdg 25.3531496180304,15.9116015622793 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 771s Parsed 76 reference bases 771s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '4' because it was < 2 characters long 771s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '9' because it was < 2 characters long 771s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '13' because it was < 2 characters long 771s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '15' because it was < 2 characters long 771s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '24' because it was < 2 characters long 771s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '30' because it was < 2 characters long 771s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '31' because it was < 2 characters long 771s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '33' because it was < 2 characters long 771s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '36' because it was < 2 characters long 771s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '44' because it was < 2 characters long 771s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '48' because it was < 2 characters long 771s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '49' because it was < 2 characters long 771s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '54' because it was < 2 characters long 771s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '55' because it was < 2 characters long 771s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '56' because it was < 2 characters long 771s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '58' because it was < 2 characters long 771s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '65' because it was < 2 characters long 771s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '71' because it was < 2 characters long 771s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '74' because it was < 2 characters long 771s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '75' because it was < 2 characters long 771s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '78' because it was < 2 characters long 771s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '79' because it was < 2 characters long 771s Read 50 alignments... 771s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '81' because it was < 2 characters long 771s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '85' because it was < 2 characters long 771s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '89' because it was < 2 characters long 771s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '90' because it was < 2 characters long 771s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '95' because it was < 2 characters long 771s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '100' because it was < 2 characters long 771s Warning: skipping mate #2 of read '103' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '103' because it was < 2 characters long 771s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '104' because it was < 2 characters long 771s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '105' because it was < 2 characters long 771s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '109' because it was < 2 characters long 771s 110 reads; of these: 771s 94 (85.45%) were paired; of these: 771s 94 (100.00%) aligned concordantly 0 times 771s 0 (0.00%) aligned concordantly exactly 1 time 771s 0 (0.00%) aligned concordantly >1 times 771s ---- 771s 94 pairs aligned concordantly 0 times; of these: 771s 0 (0.00%) aligned discordantly 1 time 771s ---- 771s 94 pairs aligned 0 times concordantly or discordantly; of these: 771s 188 mates make up the pairs; of these: 771s 188 (100.00%) aligned 0 times 771s 0 (0.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 16 (14.55%) were unpaired; of these: 771s 16 (100.00%) aligned 0 times 771s 0 (0.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 0.00% overall alignment rate 771s Read 100 alignments... 771s Read 150 alignments... 771s Read 200 alignments... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s /usr/bin/bowtie2 --trim5 5 --local --cp-ival 2 --trim3 6 --cp-min 4 --np 1 --large-index --score-min L,9.15660414812684,9.17943970125745 -R 3 -D 30 --rdg 25.3531496180304,15.9116015622793 -r -p 3 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s --- Summary --- 771s Read 1 reference strings 771s Checked 0 alignments, 0 edits 771s --------------- 771s PASSED 771s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 771s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '4' because it was < 2 characters long 771s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '9' because it was < 2 characters long 771s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '13' because it was < 2 characters long 771s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '15' because it was < 2 characters long 771s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '24' because it was < 2 characters long 771s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '30' because it was < 2 characters long 771s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '31' because it was < 2 characters long 771s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '33' because it was < 2 characters long 771s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '36' because it was < 2 characters long 771s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '44' because it was < 2 characters long 771s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '48' because it was < 2 characters long 771s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '49' because it was < 2 characters long 771s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '54' because it was < 2 characters long 771s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '55' because it was < 2 characters long 771s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '56' because it was < 2 characters long 771s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '58' because it was < 2 characters long 771s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '81' because it was < 2 characters long 771s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '85' because it was < 2 characters long 771s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '89' because it was < 2 characters long 771s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '90' because it was < 2 characters long 771s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '95' because it was < 2 characters long 771s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '100' because it was < 2 characters long 771s Warning: skipping mate #2 of read '103' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '103' because it was < 2 characters long 771s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '104' because it was < 2 characters long 771s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '105' because it was < 2 characters long 771s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '109' because it was < 2 characters long 771s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '65' because it was < 2 characters long 771s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '71' because it was < 2 characters long 771s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '74' because it was < 2 characters long 771s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '75' because it was < 2 characters long 771s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '78' because it was < 2 characters long 771s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '79' because it was < 2 characters long 771s 110 reads; of these: 771s 94 (85.45%) were paired; of these: 771s 94 (100.00%) aligned concordantly 0 times 771s 0 (0.00%) aligned concordantly exactly 1 time 771s 0 (0.00%) aligned concordantly >1 times 771s ---- 771s 94 pairs aligned concordantly 0 times; of these: 771s 0 (0.00%) aligned discordantly 1 time 771s ---- 771s 94 pairs aligned 0 times concordantly or discordantly; of these: 771s 188 mates make up the pairs; of these: 771s 188 (100.00%) aligned 0 times 771s 0 (0.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 16 (14.55%) were unpaired; of these: 771s 16 (100.00%) aligned 0 times 771s 0 (0.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 0.00% overall alignment rate 771s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 771s Flattened IUPAC characters 771s Mutating sequence Sim.pm.2 771s Introducing 19 SNPs, 0/0 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutating sequence Sim.pm.1 771s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutated reference genome to subject genome 771s SNPs introduced: 29 771s Reference gaps introduced: 0 771s Read gaps introduced: 0 771s Rearrangements introduced: 0 771s Created read sampler 771s Sampling 47 reads 771s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 771s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 771s parsing sequence Sim.pm.1... 771s parsing sequence Sim.pm.2... 771s Parsed 76 reference bases 771s *** Run 51 of 100 771s /usr/bin/bowtie2 --mm --rdg 3.80064560801484 -D 14 -k 8 --ma 17.88500135449 --score-min L,5.69560936425198,4.62336310929892 --cp-min 2 --large-index --rfg 4.93721458952094,5.31246711293222 --mp 5.09375307800668,2.62495400529406 -i S,1.89955681351122 --trim3 2 --cp-ival 1 --norc --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 771s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 771s /usr/bin/bowtie2 --mm --rdg 3.80064560801484 -D 14 -k 8 --ma 17.88500135449 --score-min L,5.69560936425198,4.62336310929892 --cp-min 2 --large-index --rfg 4.93721458952094,5.31246711293222 --mp 5.09375307800668,2.62495400529406 -i S,1.89955681351122 --trim3 2 --cp-ival 1 --norc --qseq -p 4 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 771s 47 reads; of these: 771s 47 (100.00%) were unpaired; of these: 771s 42 (89.36%) aligned 0 times 771s 4 (8.51%) aligned exactly 1 time 771s 1 (2.13%) aligned >1 times 771s 10.64% overall alignment rate 771s Read 50 alignments... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GCGATTAGTTGGAGTTCTG 771s GCGATTAGTTGGAGTTCTG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GTAGGGGCGATTAGTTGGAGT 771s GTAGGGGCGATTAGTTGGAGT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TGC 771s TGC 771s Processing line... 771s TGC 771s TGC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GCGATTAG 771s GCGATTAG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GGGTAGGGGCG 771s GGGTAGGGGCG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s --- Summary --- 771s Read 1 reference strings 771s Checked 6 alignments, 0 edits 771s --------------- 771s PASSED 771s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 771s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 771s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 771s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 771s 47 reads; of these: 771s 47 (100.00%) were unpaired; of these: 771s 42 (89.36%) aligned 0 times 771s 4 (8.51%) aligned exactly 1 time 771s 1 (2.13%) aligned >1 times 771s 10.64% overall alignment rate 771s Flattened IUPAC characters 771s Mutating sequence Sim.pm.2 771s Introducing 20 SNPs, 1/0 ref/read gaps, and 1 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutating sequence Sim.pm.1 771s Introducing 6 SNPs, 0/0 ref/read gaps, and 2 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutated reference genome to subject genome 771s SNPs introduced: 26 771s Reference gaps introduced: 1 771s Read gaps introduced: 0 771s Rearrangements introduced: 3 771s Created read sampler 771s Sampling 80 reads 771s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 771s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 771s parsing sequence Sim.pm.1... 771s parsing sequence Sim.pm.2... 771s Parsed 76 reference bases 771s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 771s *** Run 52 of 100 771s /usr/bin/bowtie2 --local --cp-ival 4 --large-index --cp-min 2 --score-min L,1.57000228690458,7.16315919294419 --trim3 9 -N 1 -L24 --mp 8.40700790686332,4.87208286492482 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 771s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 771s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #2 of read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 771s Warning: skipping mate #2 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 771s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (1) 771s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 771s Read 50 alignments... 771s Read 100 alignments... 771s 80 reads; of these: 771s 63 (78.75%) were paired; of these: 771s 63 (100.00%) aligned concordantly 0 times 771s 0 (0.00%) aligned concordantly exactly 1 time 771s 0 (0.00%) aligned concordantly >1 times 771s ---- 771s 63 pairs aligned concordantly 0 times; of these: 771s 0 (0.00%) aligned discordantly 1 time 771s ---- 771s 63 pairs aligned 0 times concordantly or discordantly; of these: 771s 126 mates make up the pairs; of these: 771s 126 (100.00%) aligned 0 times 771s 0 (0.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 17 (21.25%) were unpaired; of these: 771s 17 (100.00%) aligned 0 times 771s 0 (0.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 0.00% overall alignment rate 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s --- Summary --- 771s Read 1 reference strings 771s Checked 0 alignments, 0 edits 771s --------------- 771s PASSED 771s Flattened IUPAC characters 771s Mutating sequence Sim.pm.2 771s Introducing 11 SNPs, 1/2 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutating sequence Sim.pm.1 771s Introducing 3 SNPs, 2/1 ref/read gaps, and 1 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutated reference genome to subject genome 771s SNPs introduced: 14 771s Reference gaps introduced: 3 771s Read gaps introduced: 3 771s Rearrangements introduced: 1 771s Created read sampler 771s Sampling 74 reads 771s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 771s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 771s parsing sequence Sim.pm.1... 771s parsing sequence Sim.pm.2... 771s Parsed 76 reference bases 771s *** Run 53 of 100 771s /usr/bin/bowtie2 --local --cp-ival 1 --trim5 2 --n-ceil 1.13057282920866,1.26843437357662 --norc --nofw -N 0 -L14 --np 2 --cp-min 2 --large-index --rdg 39.1066010585339,16.146625770006 --score-min L,1.40327141540035,3.86595880221878 --gbar 1 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 771s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '15' because it was < 2 characters long 771s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '22' because it was < 2 characters long 771s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '33' because it was < 2 characters long 771s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '42' because it was < 2 characters long 771s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '54' because it was < 2 characters long 771s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '60' because it was < 2 characters long 772s 74 reads; of these: 772s 74 (100.00%) were unpaired; of these: 772s 74 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 0.00% overall alignment rate 772s Read 50 alignments... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s --- Summary --- 772s Read 1 reference strings 772s Checked 0 alignments, 0 edits 772s --------------- 772s PASSED 772s ALSO checking that bowtie2 and bowtie2-align match up 772s /usr/bin/bowtie2 --local --cp-ival 1 --trim5 2 --n-ceil 1.13057282920866,1.26843437357662 --norc --nofw -N 0 -L14 --np 2 --cp-min 2 --large-index --rdg 39.1066010585339,16.146625770006 --score-min L,1.40327141540035,3.86595880221878 --gbar 1 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 772s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '15' because it was < 2 characters long 772s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '22' because it was < 2 characters long 772s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '33' because it was < 2 characters long 772s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '42' because it was < 2 characters long 772s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '54' because it was < 2 characters long 772s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '60' because it was < 2 characters long 772s 74 reads; of these: 772s 74 (100.00%) were unpaired; of these: 772s 74 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 0.00% overall alignment rate 772s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 772s /usr/bin/bowtie2 --local --cp-ival 1 --trim5 2 --n-ceil 1.13057282920866,1.26843437357662 --norc --nofw -N 0 -L14 --np 2 --cp-min 2 --large-index --rdg 39.1066010585339,16.146625770006 --score-min L,1.40327141540035,3.86595880221878 --gbar 1 -f -p 4 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 772s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 772s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '15' because it was < 2 characters long 772s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '22' because it was < 2 characters long 772s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '33' because it was < 2 characters long 772s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '42' because it was < 2 characters long 772s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '54' because it was < 2 characters long 772s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '60' because it was < 2 characters long 772s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 772s 74 reads; of these: 772s 74 (100.00%) were unpaired; of these: 772s 74 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 0.00% overall alignment rate 772s Flattened IUPAC characters 772s Mutating sequence Sim.pm.2 772s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutating sequence Sim.pm.1 772s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutated reference genome to subject genome 772s SNPs introduced: 13 772s Reference gaps introduced: 0 772s Read gaps introduced: 0 772s Rearrangements introduced: 1 772s Created read sampler 772s Sampling 81 reads 772s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 772s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 772s parsing sequence Sim.pm.1... 772s parsing sequence Sim.pm.2... 772s Parsed 76 reference bases 772s *** Run 54 of 100 772s /usr/bin/bowtie2 --large-index --cp-min 4 --cp-ival 1 --score-min L,3.18625179018425,5.65500687047634 -k 2 --mp 2.60740783141445,1.01170441042393 --rdg 49.7218484298126,10.4280499617496 -q -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq 772s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 772s Warning: skipping read '75' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '75' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 772s Warning: skipping read '80' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '80' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 772s 81 reads; of these: 772s 81 (100.00%) were unpaired; of these: 772s 68 (83.95%) aligned 0 times 772s 10 (12.35%) aligned exactly 1 time 772s 3 (3.70%) aligned >1 times 772s 16.05% overall alignment rate 772s Read 50 alignments... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s GCT 772s GCT 772s Processing line... 772s GCT 772s GCT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TTCGGGGGTGGCTGGGGGGTAGG 772s TTCGGGGGTGGCTGGGGGGTAGG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s GCTCTCGGTTCGGGGGTGGCT 772s GCTCTCGGTTCGGGGGTGGCT 772s Processing line... 772s Processing line... 772s CTGGGG 772s CTGGGG 772s Processing line... 772s CTGGGG 772s CTGGGG 772s Processing line... 772s AGGGGCGATTAGTTG 772s AGGGGCGATTAGTTG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TTCT 772s TTCT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s GGGGTGGCTGGG 772s GGGGTGGCTGGG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TGGGGGGTAGGGGCGATT 772s TGGGGGGTAGGGGCGATT 772s Processing line... 772s AGT 772s AGT 772s Processing line... 772s AGT 772s AGT 772s Processing line... 772s GGGTG 772s GGGTG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s GAT 772s GAT 772s Processing line... 772s Processing line... 772s TGGGGGGTAGGGGCGATTAGTT 772s TGGGGGGTAGGGGCGATTAGTT 772s Processing line... 772s TCTC 772s TCTC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s --- Summary --- 772s Read 1 reference strings 772s Checked 16 alignments, 0 edits 772s --------------- 772s PASSED 772s Flattened IUPAC characters 772s Mutating sequence Sim.pm.1 772s Introducing 15 SNPs, 0/3 ref/read gaps, and 0 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutating sequence Sim.pm.2 772s Introducing 6 SNPs, 0/0 ref/read gaps, and 3 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutated reference genome to subject genome 772s SNPs introduced: 21 772s Reference gaps introduced: 0 772s Read gaps introduced: 3 772s Rearrangements introduced: 3 772s Created read sampler 772s Sampling 15 reads 772s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 772s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 772s parsing sequence Sim.pm.1... 772s parsing sequence Sim.pm.2... 772s Parsed 76 reference bases 772s *** Run 55 of 100 772s /usr/bin/bowtie2 --rfg 10.238930449965,18.969401994906 --mm -R 2 -i C --score-min L,9.04588785297259,8.38336986190939 --cp-ival 1 --trim5 5 --large-index -M 5 --cp-min 6 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq 772s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 772s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '10' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 772s 15 reads; of these: 772s 14 (93.33%) were paired; of these: 772s 14 (100.00%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 0 (0.00%) aligned concordantly >1 times 772s ---- 772s 14 pairs aligned concordantly 0 times; of these: 772s 0 (0.00%) aligned discordantly 1 time 772s ---- 772s 14 pairs aligned 0 times concordantly or discordantly; of these: 772s 28 mates make up the pairs; of these: 772s 21 (75.00%) aligned 0 times 772s 4 (14.29%) aligned exactly 1 time 772s 3 (10.71%) aligned >1 times 772s 1 (6.67%) were unpaired; of these: 772s 1 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 24.14% overall alignment rate 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TAGGGGCGATTAGTTGGAGT 772s TAGGGGCGATTAGTTGGAGT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s GCGA 772s GCGA 772s Processing line... 772s Processing line... 772s GGGGGT 772s GGGGGT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s GC 772s GC 772s Processing line... 772s GCTGGGGGGTAGGGGCGATTA 772s GCTGGGGGGTAGGGGCGATTA 772s Processing line... 772s GTTACCTG 772s GTTACCTG 772s Processing line... 772s CC 772s CC 772s Processing line... 772s Processing line... 772s --- Summary --- 772s Read 1 reference strings 772s Checked 7 alignments, 0 edits 772s --------------- 772s PASSED 772s Flattened IUPAC characters 772s Mutating sequence Sim.pm.1 772s Introducing 7 SNPs, 1/4 ref/read gaps, and 0 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutating sequence Sim.pm.2 772s Introducing 24 SNPs, 1/1 ref/read gaps, and 1 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutated reference genome to subject genome 772s SNPs introduced: 31 772s Reference gaps introduced: 2 772s Read gaps introduced: 5 772s Rearrangements introduced: 1 772s Created read sampler 772s Sampling 47 reads 772s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 772s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 772s parsing sequence Sim.pm.1... 772s parsing sequence Sim.pm.2... 772s Parsed 76 reference bases 772s *** Run 56 of 100 772s /usr/bin/bowtie2 --mm --rdg 25.7560603414965 -R 4 --score-min L,7.0557123388795,5.94077950109088 --large-index --cp-min 2 --trim3 9 --cp-ival 1 --local --trim5 7 -M 2 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 772s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 772s Warning: skipping mate #1 of read '0' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '0' because it was < 2 characters long 772s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '7' because it was < 2 characters long 772s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '9' because it was < 2 characters long 772s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '20' because it was < 2 characters long 772s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '21' because it was < 2 characters long 772s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '23' because it was < 2 characters long 772s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '26' because it was < 2 characters long 772s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '28' because it was < 2 characters long 772s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '34' because it was < 2 characters long 772s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '44' because it was < 2 characters long 772s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '46' because it was < 2 characters long 772s /usr/bin/bowtie2 --mm --rdg 25.7560603414965 -R 4 --score-min L,7.0557123388795,5.94077950109088 --large-index --cp-min 2 --trim3 9 --cp-ival 1 --local --trim5 7 -M 2 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 772s 47 reads; of these: 772s 35 (74.47%) were paired; of these: 772s 35 (100.00%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 0 (0.00%) aligned concordantly >1 times 772s ---- 772s 35 pairs aligned concordantly 0 times; of these: 772s 0 (0.00%) aligned discordantly 1 time 772s ---- 772s 35 pairs aligned 0 times concordantly or discordantly; of these: 772s 70 mates make up the pairs; of these: 772s 70 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 12 (25.53%) were unpaired; of these: 772s 12 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 0.00% overall alignment rate 772s Read 50 alignments... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s --- Summary --- 772s Read 1 reference strings 772s Checked 0 alignments, 0 edits 772s --------------- 772s PASSED 772s ALSO checking that bowtie2 and bowtie2-align match up 773s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 773s Warning: skipping mate #1 of read '0' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '0' because it was < 2 characters long 773s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '7' because it was < 2 characters long 773s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '9' because it was < 2 characters long 773s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '20' because it was < 2 characters long 773s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '21' because it was < 2 characters long 773s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '23' because it was < 2 characters long 773s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '26' because it was < 2 characters long 773s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '28' because it was < 2 characters long 773s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '34' because it was < 2 characters long 773s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '44' because it was < 2 characters long 773s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '46' because it was < 2 characters long 773s 47 reads; of these: 773s 35 (74.47%) were paired; of these: 773s 35 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 35 pairs aligned concordantly 0 times; of these: 773s 0 (0.00%) aligned discordantly 1 time 773s ---- 773s 35 pairs aligned 0 times concordantly or discordantly; of these: 773s 70 mates make up the pairs; of these: 773s 70 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 12 (25.53%) were unpaired; of these: 773s 12 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 0.00% overall alignment rate 773s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 773s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 773s /usr/bin/bowtie2 --mm --rdg 25.7560603414965 -R 4 --score-min L,7.0557123388795,5.94077950109088 --large-index --cp-min 2 --trim3 9 --cp-ival 1 --local --trim5 7 -M 2 -r -p 3 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 773s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 773s Warning: skipping mate #1 of read '0' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '0' because it was < 2 characters long 773s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '7' because it was < 2 characters long 773s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '9' because it was < 2 characters long 773s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '20' because it was < 2 characters long 773s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '21' because it was < 2 characters long 773s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '23' because it was < 2 characters long 773s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '26' because it was < 2 characters long 773s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '28' because it was < 2 characters long 773s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '34' because it was < 2 characters long 773s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '44' because it was < 2 characters long 773s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '46' because it was < 2 characters long 773s 47 reads; of these: 773s 35 (74.47%) were paired; of these: 773s 35 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 35 pairs aligned concordantly 0 times; of these: 773s 0 (0.00%) aligned discordantly 1 time 773s ---- 773s 35 pairs aligned 0 times concordantly or discordantly; of these: 773s 70 mates make up the pairs; of these: 773s 70 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 12 (25.53%) were unpaired; of these: 773s 12 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 0.00% overall alignment rate 773s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 773s Flattened IUPAC characters 773s Mutating sequence Sim.pm.1 773s Introducing 1 SNPs, 0/2 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutating sequence Sim.pm.2 773s Introducing 9 SNPs, 0/2 ref/read gaps, and 2 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutated reference genome to subject genome 773s SNPs introduced: 10 773s Reference gaps introduced: 0 773s Read gaps introduced: 4 773s Rearrangements introduced: 2 773s Created read sampler 773s Sampling 159 reads 773s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 773s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 773s *** Run 57 of 100 773s /usr/bin/bowtie2 --local --cp-ival 1 --large-index --cp-min 2 --rdg 28.5206507548016,14.2571323001088 --score-min L,6.06605137400998,9.51951308555837 --trim3 0 --mp 6.25350375685274,1.6935400697174 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 773s parsing sequence Sim.pm.1... 773s parsing sequence Sim.pm.2... 773s Parsed 76 reference bases 773s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_100_100_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 773s Read 50 alignments... 773s Read 100 alignments... 773s 159 reads; of these: 773s 159 (100.00%) were unpaired; of these: 773s 159 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 0.00% overall alignment rate 773s Read 150 alignments... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s /usr/bin/bowtie2 --local --cp-ival 1 --large-index --cp-min 2 --rdg 28.5206507548016,14.2571323001088 --score-min L,6.06605137400998,9.51951308555837 --trim3 0 --mp 6.25350375685274,1.6935400697174 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s --- Summary --- 773s Read 1 reference strings 773s Checked 0 alignments, 0 edits 773s --------------- 773s PASSED 773s ALSO checking that bowtie2 and bowtie2-align match up 773s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_100_100_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 773s 159 reads; of these: 773s 159 (100.00%) were unpaired; of these: 773s 159 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 0.00% overall alignment rate 773s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 773s Flattened IUPAC characters 773s Mutating sequence Sim.pm.1 773s Introducing 13 SNPs, 0/0 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutating sequence Sim.pm.2 773s Introducing 15 SNPs, 0/0 ref/read gaps, and 3 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutated reference genome to subject genome 773s SNPs introduced: 28 773s Reference gaps introduced: 0 773s Read gaps introduced: 0 773s Rearrangements introduced: 3 773s Created read sampler 773s Sampling 20 reads 773s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 773s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 773s parsing sequence Sim.pm.1... 773s parsing sequence Sim.pm.2... 773s Parsed 76 reference bases 773s *** Run 58 of 100 773s /usr/bin/bowtie2 --mp 7.22419256393629,3.94048341267793 -R 3 -N 1 -L22 -k 10 --trim3 8 --score-min L,1.66655493791083,4.75327859028647 --mm --rfg 25.1825554112518,4.47434164272577 --rdg 15.0468950294825,8.33774190661873 --cp-min 7 --large-index --cp-ival 1 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 773s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 773s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 773s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 773s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 773s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 773s 20 reads; of these: 773s 16 (80.00%) were paired; of these: 773s 16 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 16 pairs aligned concordantly 0 times; of these: 773s 0 (0.00%) aligned discordantly 1 time 773s ---- 773s 16 pairs aligned 0 times concordantly or discordantly; of these: 773s 32 mates make up the pairs; of these: 773s 28 (87.50%) aligned 0 times 773s 1 (3.12%) aligned exactly 1 time 773s 3 (9.38%) aligned >1 times 773s 4 (20.00%) were unpaired; of these: 773s 4 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 11.11% overall alignment rate 773s /usr/bin/bowtie2 --mp 7.22419256393629,3.94048341267793 -R 3 -N 1 -L22 -k 10 --trim3 8 --score-min L,1.66655493791083,4.75327859028647 --mm --rfg 25.1825554112518,4.47434164272577 --rdg 15.0468950294825,8.33774190661873 --cp-min 7 --large-index --cp-ival 1 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 773s Read 50 alignments... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s Processing line... 773s Processing line... 773s GGC 773s GGC 773s Processing line... 773s GGC 773s GGC 773s Processing line... 773s Processing line... 773s GGGTGGCTGGGGGGTAGGGGCGATTAGTT 773s GGGTGGCTGGGGGGTAGGGGCGATTAGTT 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s GG 773s GG 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s --- Summary --- 773s Read 1 reference strings 773s Checked 23 alignments, 0 edits 773s --------------- 773s PASSED 773s ALSO checking that bowtie2 and bowtie2-align match up 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 773s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 773s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 773s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 773s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 773s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 773s 20 reads; of these: 773s 16 (80.00%) were paired; of these: 773s 16 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 16 pairs aligned concordantly 0 times; of these: 773s 0 (0.00%) aligned discordantly 1 time 773s ---- 773s 16 pairs aligned 0 times concordantly or discordantly; of these: 773s 32 mates make up the pairs; of these: 773s 28 (87.50%) aligned 0 times 773s 1 (3.12%) aligned exactly 1 time 773s 3 (9.38%) aligned >1 times 773s 4 (20.00%) were unpaired; of these: 773s 4 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 11.11% overall alignment rate 773s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 773s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 773s /usr/bin/bowtie2 --mp 7.22419256393629,3.94048341267793 -R 3 -N 1 -L22 -k 10 --trim3 8 --score-min L,1.66655493791083,4.75327859028647 --mm --rfg 25.1825554112518,4.47434164272577 --rdg 15.0468950294825,8.33774190661873 --cp-min 7 --large-index --cp-ival 1 --qseq -p 3 -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 773s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 773s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 773s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 773s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 773s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 773s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 773s 20 reads; of these: 773s 16 (80.00%) were paired; of these: 773s 16 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 16 pairs aligned concordantly 0 times; of these: 773s 0 (0.00%) aligned discordantly 1 time 773s ---- 773s 16 pairs aligned 0 times concordantly or discordantly; of these: 773s 32 mates make up the pairs; of these: 773s 28 (87.50%) aligned 0 times 773s 1 (3.12%) aligned exactly 1 time 773s 3 (9.38%) aligned >1 times 773s 4 (20.00%) were unpaired; of these: 773s 4 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 11.11% overall alignment rate 773s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 773s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 773s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 773s /usr/bin/bowtie2 --mp 7.22419256393629,3.94048341267793 -R 3 -N 1 -L22 -k 10 --trim3 8 --score-min L,1.66655493791083,4.75327859028647 --mm --rfg 25.1825554112518,4.47434164272577 --rdg 15.0468950294825,8.33774190661873 --cp-min 7 --large-index --cp-ival 1 --qseq -p 3 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 773s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 774s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 774s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 774s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 774s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 774s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 774s 20 reads; of these: 774s 16 (80.00%) were paired; of these: 774s 16 (100.00%) aligned concordantly 0 times 774s 0 (0.00%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 16 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 16 pairs aligned 0 times concordantly or discordantly; of these: 774s 32 mates make up the pairs; of these: 774s 28 (87.50%) aligned 0 times 774s 1 (3.12%) aligned exactly 1 time 774s 3 (9.38%) aligned >1 times 774s 4 (20.00%) were unpaired; of these: 774s 4 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 11.11% overall alignment rate 774s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 774s Flattened IUPAC characters 774s Mutating sequence Sim.pm.1 774s Introducing 1 SNPs, 1/2 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutating sequence Sim.pm.2 774s Introducing 14 SNPs, 0/1 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutated reference genome to subject genome 774s SNPs introduced: 15 774s Reference gaps introduced: 1 774s Read gaps introduced: 3 774s Rearrangements introduced: 0 774s Created read sampler 774s Sampling 92 reads 774s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 774s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 774s parsing sequence Sim.pm.1... 774s parsing sequence Sim.pm.2... 774s Parsed 76 reference bases 774s *** Run 59 of 100 774s /usr/bin/bowtie2 --np 1 --cp-min 7 --large-index --score-min L,7.19921640676139,6.62153166943704 -R 3 -k 5 --rdg 10.5932076794201 --mm --cp-ival 1 -N 0 -L24 --rfg 35.8677827565752,8.09698571555493 -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw 774s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 774s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '42' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 774s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '81' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 774s Warning: skipping read '85' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '85' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 774s 92 reads; of these: 774s 92 (100.00%) were unpaired; of these: 774s 80 (86.96%) aligned 0 times 774s 7 (7.61%) aligned exactly 1 time 774s 5 (5.43%) aligned >1 times 774s 13.04% overall alignment rate 774s Read 50 alignments... 774s Read 100 alignments... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s GG 774s GG 774s Processing line... 774s GG 774s GG 774s Processing line... 774s GG 774s GG 774s Processing line... 774s GG 774s GG 774s Processing line... 774s GG 774s GG 774s Processing line... 774s Processing line... 774s /usr/bin/bowtie2 --np 1 --cp-min 7 --large-index --score-min L,7.19921640676139,6.62153166943704 -R 3 -k 5 --rdg 10.5932076794201 --mm --cp-ival 1 -N 0 -L24 --rfg 35.8677827565752,8.09698571555493 -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 774s Processing line... 774s GC 774s GC 774s Processing line... 774s GC 774s GC 774s Processing line... 774s GC 774s GC 774s Processing line... 774s GC 774s GC 774s Processing line... 774s GC 774s GC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s AT 774s AT 774s Processing line... 774s AT 774s AT 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s CGGG 774s CGGG 774s Processing line... 774s GGGC 774s GGGC 774s Processing line... 774s Processing line... 774s GGCTGGGGG 774s GGCTGGGGG 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s GGGGCGATTAG 774s GGGGCGATTAG 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s GGAG 774s GGAG 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s GGC 774s GGC 774s Processing line... 774s GGC 774s GGC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s GGC 774s GGC 774s Processing line... 774s GGC 774s GGC 774s Processing line... 774s CGGG 774s CGGG 774s Processing line... 774s Processing line... 774s CGGGGG 774s CGGGGG 774s --- Summary --- 774s Read 1 reference strings 774s Checked 23 alignments, 0 edits 774s --------------- 774s PASSED 774s ALSO checking that bowtie2 and bowtie2-align match up 774s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 774s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '42' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 774s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '81' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 774s Warning: skipping read '85' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '85' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 774s 92 reads; of these: 774s 92 (100.00%) were unpaired; of these: 774s 80 (86.96%) aligned 0 times 774s 7 (7.61%) aligned exactly 1 time 774s 5 (5.43%) aligned >1 times 774s 13.04% overall alignment rate 774s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 774s Flattened IUPAC characters 774s Mutating sequence Sim.pm.1 774s Introducing 12 SNPs, 0/0 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutating sequence Sim.pm.2 774s Introducing 6 SNPs, 1/0 ref/read gaps, and 2 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutated reference genome to subject genome 774s SNPs introduced: 18 774s Reference gaps introduced: 1 774s Read gaps introduced: 0 774s Rearrangements introduced: 2 774s Created read sampler 774s Sampling 61 reads 774s *** Run 60 of 100 774s /usr/bin/bowtie2 --score-min L,9.74691336484982,8.78658749063496 -R 1 --rdg 6.64691180874943 --mm --large-index --np 1 --cp-min 2 --mp 8.55355259406007,3.09493574177359 --rfg 5.29223888359978 -a --local --cp-ival 2 -q -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq 774s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 774s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 774s parsing sequence Sim.pm.1... 774s parsing sequence Sim.pm.2... 774s Parsed 76 reference bases 774s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '20' because it was < 2 characters long 774s /usr/bin/bowtie2 --score-min L,9.74691336484982,8.78658749063496 -R 1 --rdg 6.64691180874943 --mm --large-index --np 1 --cp-min 2 --mp 8.55355259406007,3.09493574177359 --rfg 5.29223888359978 -a --local --cp-ival 2 -q -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 774s 61 reads; of these: 774s 61 (100.00%) were unpaired; of these: 774s 61 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s Read 50 alignments... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s --- Summary --- 774s Read 1 reference strings 774s Checked 0 alignments, 0 edits 774s --------------- 774s PASSED 774s ALSO checking that bowtie2 and bowtie2-align match up 774s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '20' because it was < 2 characters long 774s 61 reads; of these: 774s 61 (100.00%) were unpaired; of these: 774s 61 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 774s Flattened IUPAC characters 774s Mutating sequence Sim.pm.1 774s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 774s *** Run 61 of 100 774s /usr/bin/bowtie2 --score-min L,8.07758490442984,2.17126392319679 -N 0 -L29 --mm --rfg 11.4640041941033 -M 2 --large-index --cp-min 2 --local --cp-ival 1 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutating sequence Sim.pm.2 774s Introducing 5 SNPs, 3/1 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutated reference genome to subject genome 774s SNPs introduced: 8 774s Reference gaps introduced: 3 774s Read gaps introduced: 2 774s Rearrangements introduced: 0 774s Created read sampler 774s Sampling 101 reads 774s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 774s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 774s parsing sequence Sim.pm.1... 774s parsing sequence Sim.pm.2... 774s Parsed 76 reference bases 774s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 774s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '3' because it was < 2 characters long 774s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '58' because it was < 2 characters long 774s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '75' because it was < 2 characters long 774s Read 50 alignments... 774s Read 100 alignments... 774s 101 reads; of these: 774s 101 (100.00%) were paired; of these: 774s 101 (100.00%) aligned concordantly 0 times 774s 0 (0.00%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 101 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 101 pairs aligned 0 times concordantly or discordantly; of these: 774s 202 mates make up the pairs; of these: 774s 202 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s Read 150 alignments... 774s Read 200 alignments... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s /usr/bin/bowtie2 --score-min L,8.07758490442984,2.17126392319679 -N 0 -L29 --mm --rfg 11.4640041941033 -M 2 --large-index --cp-min 2 --local --cp-ival 1 -f -p 3 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s --- Summary --- 774s Read 1 reference strings 774s Checked 0 alignments, 0 edits 774s --------------- 774s PASSED 774s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 774s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 774s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '3' because it was < 2 characters long 774s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '58' because it was < 2 characters long 774s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '75' because it was < 2 characters long 774s 101 reads; of these: 774s 101 (100.00%) were paired; of these: 774s 101 (100.00%) aligned concordantly 0 times 774s 0 (0.00%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 101 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 101 pairs aligned 0 times concordantly or discordantly; of these: 774s 202 mates make up the pairs; of these: 774s 202 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 774s Flattened IUPAC characters 774s Mutating sequence Sim.pm.1 774s Introducing 7 SNPs, 1/1 ref/read gaps, and 1 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutating sequence Sim.pm.2 774s Introducing 9 SNPs, 2/1 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutated reference genome to subject genome 774s SNPs introduced: 16 774s Reference gaps introduced: 3 774s Read gaps introduced: 2 774s Rearrangements introduced: 1 774s Created read sampler 774s Sampling 73 reads 774s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 774s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 774s parsing sequence Sim.pm.1... 774s parsing sequence Sim.pm.2... 774s *** Run 62 of 100 774s /usr/bin/bowtie2 --rdg 32.176349849901,17.6215378804275 --rfg 14.4156085603529 --score-min L,7.58291808913836,1.34105581882864 --ma 1.28069396543269 --cp-ival 2 --large-index --cp-min 2 --np 3 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq 774s Parsed 76 reference bases 774s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 774s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '29' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 774s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '36' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 774s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '67' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 774s Read 50 alignments... 774s Read 100 alignments... 774s 73 reads; of these: 774s 73 (100.00%) were paired; of these: 774s 73 (100.00%) aligned concordantly 0 times 774s 0 (0.00%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 73 pairs aligned concordantly 0 times; of these: 774s 2 (2.74%) aligned discordantly 1 time 774s ---- 774s 71 pairs aligned 0 times concordantly or discordantly; of these: 774s 142 mates make up the pairs; of these: 775s 130 (91.55%) aligned 0 times 775s 10 (7.04%) aligned exactly 1 time 775s 2 (1.41%) aligned >1 times 775s 10.96% overall alignment rate 775s Read 150 alignments... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s CGG 775s CGG 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s TTG 775s TTG 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s GCGATTAGTTGGAGTTC 775s GCGATTAGTTGGAGTTC 775s Processing line... 775s Processing line... 775s GTTCG 775s GTTCG 775s Processing line... 775s TGCTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCG 775s TGCTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCG 775s Processing line... 775s Processing line... 775s Processing line... 775s GGGGC 775s GGGGC 775s Processing line... 775s GGCTG 775s GGCTG 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s TAGGGGCGATTAGT 775s TAGGGGCGATTAGT 775s Processing line... 775s Processing line... 775s GTTACCT 775s GTTACCT 775s /usr/bin/bowtie2 --rdg 32.176349849901,17.6215378804275 --rfg 14.4156085603529 --score-min L,7.58291808913836,1.34105581882864 --ma 1.28069396543269 --cp-ival 2 --large-index --cp-min 2 --np 3 -q -p 4 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s AGTTGGAGTTCTGG 775s AGTTGGAGTTCTGG 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s GGTGGC 775s GGTGGC 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s CG 775s CG 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s GTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGTTGGAG 775s GTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGTTGGAG 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s TGCTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGTTGGAGTTCTG 775s TGCTCTCGGTTCGGGGGTGGCTGGGGGGTAGGGGCGATTAGTTGGAGTTCTG 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s CGATT 775s CGATT 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s CGATTAGTTGGAGTTCT 775s CGATTAGTTGGAGTTCT 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s --- Summary --- 775s Read 1 reference strings 775s Checked 16 alignments, 0 edits 775s --------------- 775s PASSED 775s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 775s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 775s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #2 of read '29' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 775s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '36' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 775s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '67' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 775s 73 reads; of these: 775s 73 (100.00%) were paired; of these: 775s 73 (100.00%) aligned concordantly 0 times 775s 0 (0.00%) aligned concordantly exactly 1 time 775s 0 (0.00%) aligned concordantly >1 times 775s ---- 775s 73 pairs aligned concordantly 0 times; of these: 775s 2 (2.74%) aligned discordantly 1 time 775s ---- 775s 71 pairs aligned 0 times concordantly or discordantly; of these: 775s 142 mates make up the pairs; of these: 775s 130 (91.55%) aligned 0 times 775s 10 (7.04%) aligned exactly 1 time 775s 2 (1.41%) aligned >1 times 775s 10.96% overall alignment rate 775s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 775s Flattened IUPAC characters 775s Mutating sequence Sim.pm.1 775s Introducing 12 SNPs, 3/0 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutating sequence Sim.pm.2 775s Introducing 5 SNPs, 0/2 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s *** Run 63 of 100 775s /usr/bin/bowtie2 --trim5 9 --n-ceil 0.457746210931068,1.18441952610186 --cp-min 2 --large-index --cp-ival 1 --local -N 0 -L13 -i C,4.57971996826874 --mp 5.3816745478857,1.47266081495963 --score-min L,1.77042154571313,5.09779543118207 --rfg 36.196208346485,15.338299251979 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq 775s Finished ref gaps 775s Finished read gaps 775s Mutated reference genome to subject genome 775s SNPs introduced: 17 775s Reference gaps introduced: 3 775s Read gaps introduced: 2 775s Rearrangements introduced: 0 775s Created read sampler 775s Sampling 130 reads 775s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 775s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 775s parsing sequence Sim.pm.1... 775s parsing sequence Sim.pm.2... 775s Parsed 76 reference bases 775s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '5' because it was < 2 characters long 775s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '7' because it was < 2 characters long 775s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '26' because it was < 2 characters long 775s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '29' because it was < 2 characters long 775s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '32' because it was < 2 characters long 775s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '48' because it was < 2 characters long 775s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '55' because it was < 2 characters long 775s Warning: skipping mate #2 of read '55' because it was < 2 characters long 775s Read 50 alignments... 775s Read 100 alignments... 775s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '69' because it was < 2 characters long 775s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '85' because it was < 2 characters long 775s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '88' because it was < 2 characters long 775s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '96' because it was < 2 characters long 775s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '97' because it was < 2 characters long 775s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '98' because it was < 2 characters long 775s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '101' because it was < 2 characters long 775s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '107' because it was < 2 characters long 775s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '113' because it was < 2 characters long 775s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '117' because it was < 2 characters long 775s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '119' because it was < 2 characters long 775s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '121' because it was < 2 characters long 775s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '128' because it was < 2 characters long 775s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '130' because it was < 2 characters long 775s Read 150 alignments... 775s 130 reads; of these: 775s 109 (83.85%) were paired; of these: 775s 109 (100.00%) aligned concordantly 0 times 775s 0 (0.00%) aligned concordantly exactly 1 time 775s 0 (0.00%) aligned concordantly >1 times 775s ---- 775s 109 pairs aligned concordantly 0 times; of these: 775s 0 (0.00%) aligned discordantly 1 time 775s ---- 775s 109 pairs aligned 0 times concordantly or discordantly; of these: 775s 218 mates make up the pairs; of these: 775s 218 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 21 (16.15% Read 200 alignments... 775s ) were unpaired; of these: 775s 21 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing 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line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s --- Summary --- 775s Read 1 reference strings 775s Checked 0 alignments, 0 edits 775s --------------- 775s PASSED 775s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 775s /usr/bin/bowtie2 --trim5 9 --n-ceil 0.457746210931068,1.18441952610186 --cp-min 2 --large-index --cp-ival 1 --local -N 0 -L13 -i C,4.57971996826874 --mp 5.3816745478857,1.47266081495963 --score-min L,1.77042154571313,5.09779543118207 --rfg 36.196208346485,15.338299251979 -q -p 2 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 775s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '5' because it was < 2 characters long 775s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '7' because it was < 2 characters long 775s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '26' because it was < 2 characters long 775s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '29' because it was < 2 characters long 775s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '32' because it was < 2 characters long 775s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '48' because it was < 2 characters long 775s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #2 of read '55' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '55' because it was < 2 characters long 775s Warning: skipping mate #2 of read '55' because it was < 2 characters long 775s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '69' because it was < 2 characters long 775s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '85' because it was < 2 characters long 775s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '88' because it was < 2 characters long 775s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '96' because it was < 2 characters long 775s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '97' because it was < 2 characters long 775s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '98' because it was < 2 characters long 775s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '101' because it was < 2 characters long 775s Warning: skipping mate #1 of read '107' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '107' because it was < 2 characters long 775s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '113' because it was < 2 characters long 775s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '117' because it was < 2 characters long 775s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '119' because it was < 2 characters long 775s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '121' because it was < 2 characters long 775s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '128' because it was < 2 characters long 775s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '130' because it was < 2 characters long 775s 130 reads; of these: 775s 109 (83.85%) were paired; of these: 775s 109 (100.00%) aligned concordantly 0 times 775s 0 (0.00%) aligned concordantly exactly 1 time 775s 0 (0.00%) aligned concordantly >1 times 775s ---- 775s 109 pairs aligned concordantly 0 times; of these: 775s 0 (0.00%) aligned discordantly 1 time 775s ---- 775s 109 pairs aligned 0 times concordantly or discordantly; of these: 775s 218 mates make up the pairs; of these: 775s 218 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 21 (16.15%) were unpaired; of these: 775s 21 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 775s Flattened IUPAC characters 775s Mutating sequence Sim.pm.2 775s Introducing 12 SNPs, 2/0 ref/read gaps, and 2 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutating sequence Sim.pm.1 775s Introducing 12 SNPs, 3/0 ref/read gaps, and 1 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutated reference genome to subject genome 775s SNPs introduced: 24 775s Reference gaps introduced: 5 775s Read gaps introduced: 0 775s Rearrangements introduced: 3 775s Created read sampler 775s Sampling 17 reads 775s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 775s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 775s parsing sequence Sim.pm.1... 775s *** Run 64 of 100 775s /usr/bin/bowtie2 --mm --rfg 46.6373739620563 --score-min L,1.59527132036074,2.91642504366866 --trim3 0 --gbar 1 -N 1 -L26 --local --cp-ival 1 -M 13 --large-index --cp-min 10 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 775s parsing sequence Sim.pm.2... 775s Parsed 76 reference bases 775s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 775s 17 reads; of these: 775s 17 (100.00%) were paired; of these: 775s 17 (100.00%) aligned concordantly 0 times 775s 0 (0.00%) aligned concordantly exactly 1 time 775s 0 (0.00%) aligned concordantly >1 times 775s ---- 775s 17 pairs aligned concordantly 0 times; of these: 775s 0 (0.00%) aligned discordantly 1 time 775s ---- 775s 17 pairs aligned 0 times concordantly or discordantly; of these: 775s 34 mates make up the pairs; of these: 775s 34 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s /usr/bin/bowtie2 --mm --rfg 46.6373739620563 --score-min L,1.59527132036074,2.91642504366866 --trim3 0 --gbar 1 -N 1 -L26 --local --cp-ival 1 -M 13 --large-index --cp-min 10 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 775s --- Summary --- 775s Read 1 reference strings 775s Checked 0 alignments, 0 edits 775s --------------- 775s PASSED 775s ALSO checking that bowtie2 and bowtie2-align match up 775s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 775s 17 reads; of these: 775s 17 (100.00%) were paired; of these: 775s 17 (100.00%) aligned concordantly 0 times 775s 0 (0.00%) aligned concordantly exactly 1 time 775s 0 (0.00%) aligned concordantly >1 times 775s ---- 775s 17 pairs aligned concordantly 0 times; of these: 775s 0 (0.00%) aligned discordantly 1 time 775s ---- 775s 17 pairs aligned 0 times concordantly or discordantly; of these: 775s 34 mates make up the pairs; of these: 775s 34 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 775s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 775s /usr/bin/bowtie2 --mm --rfg 46.6373739620563 --score-min L,1.59527132036074,2.91642504366866 --trim3 0 --gbar 1 -N 1 -L26 --local --cp-ival 1 -M 13 --large-index --cp-min 10 -r -p 4 -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 775s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 775s 17 reads; of these: 775s 17 (100.00%) were paired; of these: 775s 17 (100.00%) aligned concordantly 0 times 775s 0 (0.00%) aligned concordantly exactly 1 time 775s 0 (0.00%) aligned concordantly >1 times 775s ---- 775s 17 pairs aligned concordantly 0 times; of these: 775s 0 (0.00%) aligned discordantly 1 time 775s ---- 775s 17 pairs aligned 0 times concordantly or discordantly; of these: 775s 34 mates make up the pairs; of these: 775s 34 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 775s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 775s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 775s Flattened IUPAC characters 775s Mutating sequence Sim.pm.2 775s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutating sequence Sim.pm.1 775s Introducing 2 SNPs, 3/1 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutated reference genome to subject genome 775s SNPs introduced: 8 775s Reference gaps introduced: 3 775s Read gaps introduced: 1 775s Rearrangements introduced: 1 775s Created read sampler 775s Sampling 153 reads 775s *** Run 65 of 100 775s /usr/bin/bowtie2 --mm --rfg 33.646579167321,9.86032690812265 -k 9 --score-min L,2.19299120009144,8.3320517624842 --trim3 6 --nofw --cp-ival 3 --local --trim5 4 --large-index --cp-min 3 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 775s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 775s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 775s parsing sequence Sim.pm.1... 775s parsing sequence Sim.pm.2... 775s Parsed 76 reference bases 775s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 775s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 775s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 775s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #2 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 775s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 775s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 775s Warning: skipping mate #2 of read 'R_1_1_1_124_124_1/1' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #2 of read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 775s Warning: skipping read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #2 of read 'R_1_1_1_128_128_1/1' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 775s Warning: skipping mate #2 of read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 775s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_139_139_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_141_141_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 775s Read 50 alignments... 775s Read 100 alignments... 775s Read 150 alignments... 775s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because it was < 2 characters long 775s Warning: skipping read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 775s Warning: skipping mate #1 of read 'R_1_1_1_153_153_1/1' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read 'R_1_1_1_153_153_1/1' because it was < 2 characters long 775s 153 reads; of these: 775s 122 (79.74%) were paired; of these: 775s 122 (100.00%) aligned concordantly 0 times 775s 0 (0.00%) aligned concordantly exactly 1 time 775s 0 (0.00%) aligned concordantly >1 times 775s ---- 775s 122 pairs aligned concordantly 0 times; of these: 775s 0 (0.00%) aligned discordantly 1 time 775s ---- 775s 122 pairs aligned 0 times concordantly or discordantly; of these: 775s 244 mates make up the pairs; of these: 775s 244 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 31 (20.26%) were unpaired; of these: 775s 31 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s Read 200 alignments... 775s Read 250 alignments... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s 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line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s --- Summary --- 775s Read 1 reference strings 775s Checked 0 alignments, 0 edits 775s --------------- 775s PASSED 775s Flattened IUPAC characters 775s Mutating sequence Sim.pm.1 775s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutating sequence Sim.pm.2 775s Introducing 7 SNPs, 1/1 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutated reference genome to subject genome 775s SNPs introduced: 8 775s Reference gaps introduced: 2 775s Read gaps introduced: 1 775s Rearrangements introduced: 0 775s Created read sampler 775s Sampling 124 reads 775s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 775s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 775s parsing sequence Sim.pm.1... 775s parsing sequence Sim.pm.2... 775s Parsed 76 reference bases 775s *** Run 66 of 100 775s /usr/bin/bowtie2 --np 6 --cp-min 4 --large-index --ma 2.44526630632935 --score-min L,1.5455884129624,2.22008048962189 --mm --trim5 7 --n-ceil 0.516368715274772,0.301922899048518 --norc --cp-ival 1 --trim3 6 --mp 3.47788576438105,1.66448669064854 --rfg 43.5587889400763,5.47149594131725 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 776s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 776s 124 reads; of these: 776s 124 (100.00%) were unpaired; of these: 776s 120 (96.77%) aligned 0 times 776s 1 (0.81%) aligned exactly 1 time 776s 3 (2.42%) aligned >1 times 776s 3.23% overall alignment rate 776s Read 50 alignments... 776s Read 100 alignments... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GG 776s GG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GT 776s GT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GGT 776s GGT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GGGGGTA 776s GGGGGTA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s --- Summary --- 776s Read 1 reference strings 776s Checked 4 alignments, 0 edits 776s --------------- 776s PASSED 776s ALSO checking that bowtie2 and bowtie2-align match up 776s /usr/bin/bowtie2 --np 6 --cp-min 4 --large-index --ma 2.44526630632935 --score-min L,1.5455884129624,2.22008048962189 --mm --trim5 7 --n-ceil 0.516368715274772,0.301922899048518 --norc --cp-ival 1 --trim3 6 --mp 3.47788576438105,1.66448669064854 --rfg 43.5587889400763,5.47149594131725 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 776s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 776s 124 reads; of these: 776s 124 (100.00%) were unpaired; of these: 776s 120 (96.77%) aligned 0 times 776s 1 (0.81%) aligned exactly 1 time 776s 3 (2.42%) aligned >1 times 776s 3.23% overall alignment rate 776s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 776s Flattened IUPAC characters 776s Mutating sequence Sim.pm.1 776s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutating sequence Sim.pm.2 776s Introducing 1 SNPs, 0/2 ref/read gaps, and 3 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutated reference genome to subject genome 776s SNPs introduced: 6 776s Reference gaps introduced: 0 776s Read gaps introduced: 2 776s Rearrangements introduced: 4 776s Created read sampler 776s Sampling 62 reads 776s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 776s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 776s parsing sequence Sim.pm.1... 776s parsing sequence Sim.pm.2... 776s Parsed 76 reference bases 776s *** Run 67 of 100 776s /usr/bin/bowtie2 --norc --cp-ival 2 --trim3 0 --nofw -N 1 -L13 -i C,4.75989529145467,12.2805725270178 --rfg 36.2829858316359,2.95565533835008 --large-index --np 3 --cp-min 2 --score-min L,8.59935612601474,9.50154900254294 -D 15 --gbar 5 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 776s 62 reads; of these: 776s 62 (100.00%) were unpaired; of these: 776s 62 (100.00%) aligned 0 times 776s 0 (0.00%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 0.00% overall alignment rate 776s Read 50 alignments... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s --- Summary --- 776s Read 1 reference strings 776s Checked 0 alignments, 0 edits 776s --------------- 776s PASSED 776s /usr/bin/bowtie2 --norc --cp-ival 2 --trim3 0 --nofw -N 1 -L13 -i C,4.75989529145467,12.2805725270178 --rfg 36.2829858316359,2.95565533835008 --large-index --np 3 --cp-min 2 --score-min L,8.59935612601474,9.50154900254294 -D 15 --gbar 5 --qseq -p 2 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 776s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 776s 62 reads; of these: 776s 62 (100.00%) were unpaired; of these: 776s 62 (100.00%) aligned 0 times 776s 0 (0.00%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 0.00% overall alignment rate 776s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 776s Flattened IUPAC characters 776s Mutating sequence Sim.pm.1 776s Introducing 1 SNPs, 1/0 ref/read gaps, and 2 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutating sequence Sim.pm.2 776s Introducing 17 SNPs, 3/0 ref/read gaps, and 0 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutated reference genome to subject genome 776s SNPs introduced: 18 776s Reference gaps introduced: 4 776s Read gaps introduced: 0 776s Rearrangements introduced: 2 776s Created read sampler 776s Sampling 110 reads 776s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 776s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 776s parsing sequence Sim.pm.1... 776s parsing sequence Sim.pm.2... 776s Parsed 76 reference bases 776s *** Run 68 of 100 776s /usr/bin/bowtie2 --cp-ival 4 --trim5 2 --n-ceil 1.02198620809653,1.00819928441054 --rfg 37.8311078337227 --nofw --trim3 6 --mp 3.37770610866371,2.96119032180923 --cp-min 2 --large-index --rdg 20.1666064523913 --ma 30.5480032104907 --score-min L,9.28591962312496,1.42395092921137 --gbar 4 -D 26 -k 4 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 776s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 776s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '11' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 776s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '15' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 776s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '18' because it was < 2 characters long 776s Warning: skipping mate #2 of read '18' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 776s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '20' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 776s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '24' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 776s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '36' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 776s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '49' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 776s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '53' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 776s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '58' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 776s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '61' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 776s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '64' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 776s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '66' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 776s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read '75' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 776s Read 50 alignments... 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 776s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '83' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 776s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '89' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 776s Warning: skipping mate #1 of read '90' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '90' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 776s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '96' because it was < 2 characters long 776s Read 100 alignments... 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 776s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '106' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 776s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '109' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 776s 110 reads; of these: 776s 92 (83.64%) were paired; of these: 776s 92 (100.00%) aligned concordantly 0 times 776s 0 (0.00%) aligned concordantly exactly 1 time 776s 0 (0.00%) aligned concordantly >1 times 776s ---- 776s 92 pairs aligned concordantly 0 times; of these: 776s 0 (0.00%) aligned discordantly 1 time 776s ---- 776s 92 pairs aligned 0 times concordantly or discordantly; of these: 776s 184 mates make up the pairs; of these: 776s 171 (92.93%) aligned 0 times 776s 3 (1.63%) aligned exactly 1 time 776s 10 (5.43%) aligned >1 times 776s 18 (16.36%) were unpaired; of these: 776s 18 (100.00%) aligned 0 times 776s 0 (0.00%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 6.44% overall alignment rate 776s Read 150 alignments... 776s Read 200 alignments... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TGG 776s TGG 776s Processing line... 776s TGG 776s TGG 776s Processing line... 776s TGG 776s TGG 776s Processing line... 776s TGG 776s TGG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GGG 776s GGG 776s Processing line... 776s GGG 776s GGG 776s Processing line... 776s GGG 776s GGG 776s Processing line... 776s GGG 776s GGG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TT 776s TT 776s Processing line... 776s TT 776s TT 776s Processing line... 776s TT 776s TT 776s Processing line... 776s TT 776s TT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s CG 776s CG 776s Processing line... 776s CG 776s CG 776s Processing line... 776s CG 776s CG 776s Processing line... 776s CG 776s CG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TA 776s TA 776s Processing line... 776s TA 776s TA 776s Processing line... 776s TA 776s TA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GGAGTT 776s GGAGTT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GGGG 776s GGGG 776s Processing line... 776s GGGG 776s GGGG 776s Processing line... 776s GGGG 776s GGGG 776s Processing line... 776s GGGG 776s GGGG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GTTGGA 776s GTTGGA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GG 776s GG 776s Processing line... 776s GG 776s GG 776s Processing line... 776s GG 776s GG 776s Processing line... 776s GG 776s GG 776s Processing line... 776s Processing line... 776s GGG 776s GGG 776s Processing line... 776s GGG 776s GGG 776s Processing line... 776s GGG 776s GGG 776s Processing line... 776s GGG 776s GGG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s CT 776s CT 776s Processing line... 776s CT 776s CT 776s Processing line... 776s CT 776s CT 776s Processing line... 776s CT 776s CT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TCG 776s TCG 776s Processing line... 776s TCG 776s TCG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GGAGTTCT 776s GGAGTTCT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s --- Summary --- 776s Read 1 reference strings 776s Checked 40 alignments, 0 edits 776s --------------- 776s PASSED 776s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 776s /usr/bin/bowtie2 --cp-ival 4 --trim5 2 --n-ceil 1.02198620809653,1.00819928441054 --rfg 37.8311078337227 --nofw --trim3 6 --mp 3.37770610866371,2.96119032180923 --cp-min 2 --large-index --rdg 20.1666064523913 --ma 30.5480032104907 --score-min L,9.28591962312496,1.42395092921137 --gbar 4 -D 26 -k 4 -f -p 2 -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 776s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 776s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '11' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 776s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '15' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 776s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '18' because it was < 2 characters long 776s Warning: skipping mate #2 of read '18' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 776s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '20' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 776s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '24' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 776s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '36' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 776s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '49' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 776s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '53' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 776s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '58' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 776s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '61' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 776s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '64' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 776s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '66' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 776s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read '75' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 776s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '83' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 776s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '89' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 776s Warning: skipping mate #1 of read '90' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '90' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 776s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '96' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 776s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '106' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 776s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '109' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 776s 110 reads; of these: 776s 92 (83.64%) were paired; of these: 776s 92 (100.00%) aligned concordantly 0 times 776s 0 (0.00%) aligned concordantly exactly 1 time 776s 0 (0.00%) aligned concordantly >1 times 776s ---- 776s 92 pairs aligned concordantly 0 times; of these: 776s 0 (0.00%) aligned discordantly 1 time 776s ---- 776s 92 pairs aligned 0 times concordantly or discordantly; of these: 776s 184 mates make up the pairs; of these: 776s 171 (92.93%) aligned 0 times 776s 3 (1.63%) aligned exactly 1 time 776s 10 (5.43%) aligned >1 times 776s 18 (16.36%) were unpaired; of these: 776s 18 (100.00%) aligned 0 times 776s 0 (0.00%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 6.44% overall alignment rate 776s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 776s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 776s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 776s Flattened IUPAC characters 776s Mutating sequence Sim.pm.2 776s Introducing 7 SNPs, 0/0 ref/read gaps, and 3 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutating sequence Sim.pm.1 776s Introducing 22 SNPs, 1/0 ref/read gaps, and 4 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutated reference genome to subject genome 776s SNPs introduced: 29 776s Reference gaps introduced: 1 776s Read gaps introduced: 0 776s Rearrangements introduced: 7 776s Created read sampler 776s Sampling 84 reads 776s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 776s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 776s parsing sequence Sim.pm.1... 776s parsing sequence Sim.pm.2... 776s Parsed 76 reference bases 776s *** Run 69 of 100 776s /usr/bin/bowtie2 --norc --trim5 6 --large-index --np 1 --cp-min 6 --cp-ival 1 -D 36 --score-min L,4.80606250023251,1.97244717956428 --nofw --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 776s 84 reads; of these: 776s 84 (100.00%) were unpaired; of these: 776s 84 (100.00%) aligned 0 times 776s 0 (0.00%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 0.00% overall alignment rate 776s Read 50 alignments... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s --- Summary --- 776s Read 1 reference strings 776s Checked 0 alignments, 0 edits 776s --------------- 776s PASSED 776s Flattened IUPAC characters 776s Mutating sequence Sim.pm.1 776s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutating sequence Sim.pm.2 776s Introducing 9 SNPs, 1/1 ref/read gaps, and 0 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutated reference genome to subject genome 776s SNPs introduced: 19 776s Reference gaps introduced: 1 776s Read gaps introduced: 1 776s Rearrangements introduced: 0 776s Created read sampler 776s Sampling 13 reads 776s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 776s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 776s parsing sequence Sim.pm.1... 776s parsing sequence Sim.pm.2... 776s Parsed 76 reference bases 776s *** Run 70 of 100 776s /usr/bin/bowtie2 --mm --score-min L,1.19449352125262,7.44564088707765 --cp-ival 2 --trim5 4 -M 3 --large-index --np 1 --cp-min 2 -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw 777s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 777s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 777s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '12' because it was < 2 characters long 777s 13 reads; of these: 777s 13 (100.00%) were unpaired; of these: 777s 11 (84.62%) aligned 0 times 777s 1 (7.69%) aligned exactly 1 time 777s 1 (7.69%) aligned >1 times 777s 15.38% overall alignment rate 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GGGGT 777s GGGGT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s CTCGGTT 777s CTCGGTT 777s Processing line... 777s Processing line... 777s Processing line... 777s --- Summary --- 777s Read 1 reference strings 777s Checked 2 alignments, 0 edits 777s --------------- 777s PASSED 777s Flattened IUPAC characters 777s Mutating sequence Sim.pm.2 777s Introducing 10 SNPs, 2/0 ref/read gaps, and 1 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutating sequence Sim.pm.1 777s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutated reference genome to subject genome 777s SNPs introduced: 16 777s Reference gaps introduced: 2 777s Read gaps introduced: 1 777s Rearrangements introduced: 1 777s Created read sampler 777s Sampling 104 reads 777s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 777s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 777s parsing sequence Sim.pm.1... 777s parsing sequence Sim.pm.2... 777s Parsed 76 reference bases 777s *** Run 71 of 100 777s /usr/bin/bowtie2 --large-index --np 1 --cp-min 6 --mm --rdg 8.87300475696354 -k 7 --score-min L,6.46523562657881,2.95011712320147 --ma 12.6784497716782 --cp-ival 1 --rfg 2.24959042864628 -N 1 -L13 --mp 7.50077643225249,5.97132075604157 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 777s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 777s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #2 of read '23' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 777s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '52' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 777s Read 50 alignments... 777s Read 100 alignments... 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 777s Warning: skipping mate #1 of read '83' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '83' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 777s Warning: skipping mate #1 of read '84' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '84' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 777s Read 150 alignments... 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 777s Read 200 alignments... 777s 104 reads; of these: 777s 104 (100.00%) were paired; of these: 777s 104 (100.00%) aligned concordantly 0 times 777s 0 (0.00%) aligned concordantly exactly 1 time 777s 0 (0.00%) aligned concordantly >1 times 777s ---- 777s 104 pairs aligned concordantly 0 times; of these: 777s 0 (0.00%) aligned discordantly 1 time 777s ---- 777s 104 pairs aligned 0 times concordantly or discordantly; of these: 777s 208 mates make up the pairs; of these: 777s 189 (90.87%) aligned 0 times 777s 7 (3.37%) aligned exactly 1 time 777s 12 (5.77%) aligned >1 times 777s 9.13% overall alignment rate 777s Read 250 alignments... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GGC 777s GGC 777s Processing line... 777s GGC 777s GGC 777s Processing line... 777s Processing line... 777s GGGGGGTAGGGGCGATTAGTTG 777s GGGGGGTAGGGGCGATTAGTTG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GGGG 777s GGGG 777s Processing line... 777s GGGG 777s GGGG 777s Processing line... 777s GGGG 777s GGGG 777s Processing line... 777s GGGG 777s GGGG 777s Processing line... 777s GGGG 777s GGGG 777s Processing line... 777s GGGG 777s GGGG 777s Processing line... 777s GGGG 777s GGGG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s CG 777s CG 777s Processing line... 777s CG 777s CG 777s Processing line... 777s CG 777s CG 777s Processing line... 777s CG 777s CG 777s Processing line... 777s CG 777s CG 777s Processing line... 777s CG 777s CG 777s Processing line... 777s CG 777s CG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GG 777s GG 777s Processing line... 777s GG 777s GG 777s Processing line... 777s GG 777s GG 777s Processing line... 777s GG 777s GG 777s Processing line... 777s GG 777s GG 777s Processing line... 777s GG 777s GG 777s Processing line... 777s GG 777s GG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GGTG 777s GGTG 777s Processing line... 777s GGTG 777s GGTG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GTG 777s GTG 777s Processing line... 777s GTG 777s GTG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GT 777s GT 777s Processing line... 777s GT 777s GT 777s Processing line... 777s GT 777s GT 777s Processing line... 777s GT 777s GT 777s Processing line... 777s GT 777s GT 777s Processing line... 777s GT 777s GT 777s Processing line... 777s GT 777s GT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GG 777s GG 777s Processing line... 777s /usr/bin/bowtie2 --large-index --np 1 --cp-min 6 --mm --rdg 8.87300475696354 -k 7 --score-min L,6.46523562657881,2.95011712320147 --ma 12.6784497716782 --cp-ival 1 --rfg 2.24959042864628 -N 1 -L13 --mp 7.50077643225249,5.97132075604157 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 777s GG 777s GG 777s Processing line... 777s GG 777s GG 777s Processing line... 777s GG 777s GG 777s Processing line... 777s GG 777s GG 777s Processing line... 777s GG 777s GG 777s Processing line... 777s GG 777s GG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s TAGTTGGAGTTCT 777s TAGTTGGAGTTCT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GT 777s GT 777s Processing line... 777s GT 777s GT 777s Processing line... 777s AC 777s AC 777s Processing line... 777s GT 777s GT 777s Processing line... 777s GT 777s GT 777s Processing line... 777s GT 777s GT 777s Processing line... 777s GT 777s GT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s TCGGTTC 777s TCGGTTC 777s Processing line... 777s Processing line... 777s TGCTCTCGGTTCGGGG 777s TGCTCTCGGTTCGGGG 777s Processing line... 777s Processing line... 777s GCTGGGGGGTAGGG 777s GCTGGGGGGTAGGG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s TTAGTTGGAGTTC 777s TTAGTTGGAGTTC 777s Processing line... 777s Processing line... 777s TG 777s TG 777s Processing line... 777s TG 777s TG 777s Processing line... 777s TG 777s TG 777s Processing line... 777s TG 777s TG 777s Processing line... 777s TG 777s TG 777s Processing line... 777s TG 777s TG 777s Processing line... 777s TG 777s TG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s CGG 777s CGG 777s Processing line... 777s CGG 777s CGG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GGGGGTG 777s GGGGGTG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s CTGG 777s CTGG 777s Processing line... 777s CTGG 777s CTGG 777s Processing line... 777s CTGG 777s CTGG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s --- Summary --- 777s Read 1 reference strings 777s Checked 67 alignments, 0 edits 777s --------------- 777s PASSED 777s ALSO checking that bowtie2 and bowtie2-align match up 777s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 777s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #2 of read '23' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 777s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '52' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 777s Warning: skipping mate #1 of read '83' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '83' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 777s Warning: skipping mate #1 of read '84' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '84' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 777s 104 reads; of these: 777s 104 (100.00%) were paired; of these: 777s 104 (100.00%) aligned concordantly 0 times 777s 0 (0.00%) aligned concordantly exactly 1 time 777s 0 (0.00%) aligned concordantly >1 times 777s ---- 777s 104 pairs aligned concordantly 0 times; of these: 777s 0 (0.00%) aligned discordantly 1 time 777s ---- 777s 104 pairs aligned 0 times concordantly or discordantly; of these: 777s 208 mates make up the pairs; of these: 777s 189 (90.87%) aligned 0 times 777s 7 (3.37%) aligned exactly 1 time 777s 12 (5.77%) aligned >1 times 777s 9.13% overall alignment rate 777s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 777s Flattened IUPAC characters 777s Mutating sequence Sim.pm.1 777s Introducing 16 SNPs, 1/1 ref/read gaps, and 0 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutating sequence Sim.pm.2 777s Introducing 11 SNPs, 1/1 ref/read gaps, and 1 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutated reference genome to subject genome 777s SNPs introduced: 27 777s Reference gaps introduced: 2 777s Read gaps introduced: 2 777s Rearrangements introduced: 1 777s *** Run 72 of 100 777s /usr/bin/bowtie2 --cp-min 2 --np 1 --large-index --score-min L,4.56759313365697,6.02035837840776 -k 2 --local --cp-ival 2 --rfg 42.5494993853883 --trim3 0 -N 0 -L17 --mp 8.37574538073426,1.55025756069082 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 777s Created read sampler 777s Sampling 102 reads 777s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 777s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 777s parsing sequence Sim.pm.1... 777s parsing sequence Sim.pm.2... 777s Parsed 76 reference bases 777s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '40' because it was < 2 characters long 777s Warning: skipping read '80' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '80' because it was < 2 characters long 777s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '81' because it was < 2 characters long 777s 102 reads; of these: 777s 102 (100.00%) were unpaired; of these: 777s 102 (100.00%) aligned 0 times 777s 0 (0.00%) aligned exactly 1 time 777s 0 (0.00%) aligned >1 times 777s 0.00% overall alignment rate 777s Read 50 alignments... 777s Read 100 alignments... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s /usr/bin/bowtie2 --cp-min 2 --np 1 --large-index --score-min L,4.56759313365697,6.02035837840776 -k 2 --local --cp-ival 2 --rfg 42.5494993853883 --trim3 0 -N 0 -L17 --mp 8.37574538073426,1.55025756069082 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s --- Summary --- 777s Read 1 reference strings 777s Checked 0 alignments, 0 edits 777s --------------- 777s PASSED 777s ALSO checking that bowtie2 and bowtie2-align match up 777s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '40' because it was < 2 characters long 777s Warning: skipping read '80' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '80' because it was < 2 characters long 777s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '81' because it was < 2 characters long 777s 102 reads; of these: 777s 102 (100.00%) were unpaired; of these: 777s 102 (100.00%) aligned 0 times 777s 0 (0.00%) aligned exactly 1 time 777s 0 (0.00%) aligned >1 times 777s 0.00% overall alignment rate 777s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 777s /usr/bin/bowtie2 --cp-min 2 --np 1 --large-index --score-min L,4.56759313365697,6.02035837840776 -k 2 --local --cp-ival 2 --rfg 42.5494993853883 --trim3 0 -N 0 -L17 --mp 8.37574538073426,1.55025756069082 -f -p 3 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 777s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 777s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '40' because it was < 2 characters long 777s Warning: skipping read '80' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '80' because it was < 2 characters long 777s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '81' because it was < 2 characters long 777s 102 reads; of these: 777s 102 (100.00%) were unpaired; of these: 777s 102 (100.00%) aligned 0 times 777s 0 (0.00%) aligned exactly 1 time 777s 0 (0.00%) aligned >1 times 777s 0.00% overall alignment rate 777s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 777s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 777s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 777s /usr/bin/bowtie2 --cp-min 2 --np 1 --large-index --score-min L,4.56759313365697,6.02035837840776 -k 2 --local --cp-ival 2 --rfg 42.5494993853883 --trim3 0 -N 0 -L17 --mp 8.37574538073426,1.55025756069082 -f -p 2 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 777s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 777s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '40' because it was < 2 characters long 777s Warning: skipping read '80' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '80' because it was < 2 characters long 777s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '81' because it was < 2 characters long 777s 102 reads; of these: 777s 102 (100.00%) were unpaired; of these: 777s 102 (100.00%) aligned 0 times 777s 0 (0.00%) aligned exactly 1 time 777s 0 (0.00%) aligned >1 times 777s 0.00% overall alignment rate 777s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 777s Flattened IUPAC characters 777s Mutating sequence Sim.pm.2 777s Introducing 12 SNPs, 0/3 ref/read gaps, and 0 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutating sequence Sim.pm.1 777s Introducing 15 SNPs, 0/1 ref/read gaps, and 0 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutated reference genome to subject genome 777s SNPs introduced: 27 777s Reference gaps introduced: 0 777s Read gaps introduced: 4 777s Rearrangements introduced: 0 777s Created read sampler 777s Sampling 52 reads 777s *** Run 73 of 100 777s /usr/bin/bowtie2 --large-index --cp-min 5 --rdg 40.4050608675136,14.0212528159872 -D 48 --score-min L,2.61337992089675,7.88937141541232 --cp-ival 1 --local --trim5 0 -a --rfg 21.8057020830385 --mp 8.6485848473989,3.72787841263677 --nofw -q -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq 777s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 777s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 777s parsing sequence Sim.pm.1... 777s parsing sequence Sim.pm.2... 777s Parsed 76 reference bases 777s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '28' because it was < 2 characters long 777s 52 reads; of these: 777s 52 (100.00%) were unpaired; of these: 777s 52 (100.00%) aligned 0 times 777s 0 (0.00%) aligned exactly 1 time 777s 0 (0.00%) aligned >1 times 777s 0.00% overall alignment rate 777s Read 50 alignments... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s --- Summary --- 777s Read 1 reference strings 777s Checked 0 alignments, 0 edits 777s --------------- 777s PASSED 777s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 777s /usr/bin/bowtie2 --large-index --cp-min 5 --rdg 40.4050608675136,14.0212528159872 -D 48 --score-min L,2.61337992089675,7.88937141541232 --cp-ival 1 --local --trim5 0 -a --rfg 21.8057020830385 --mp 8.6485848473989,3.72787841263677 --nofw -q -p 3 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 777s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '28' because it was < 2 characters long 779s 52 reads; of these: 779s 52 (100.00%) were unpaired; of these: 779s 52 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 0.00% overall alignment rate 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 779s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 779s *** Run 74 of 100 779s /usr/bin/bowtie2 --trim3 6 -i S,0.784915265030133 --local --cp-ival 2 --norc --trim5 9 --mm --score-min L,3.82784553261794,4.16371298670564 -R 4 --cp-min 3 --np 5 --large-index -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 779s *** Run 75 of 100 779s /usr/bin/bowtie2 --large-index --cp-min 3 --gbar 1 -R 1 --score-min L,7.48219220153351,6.73516711336058 --mm -a --cp-ival 1 --local --trim3 4 --rfg 48.6300059638687 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 779s /usr/bin/bowtie2 --large-index --cp-min 3 --gbar 1 -R 1 --score-min L,7.48219220153351,6.73516711336058 --mm -a --cp-ival 1 --local --trim3 4 --rfg 48.6300059638687 -r -p 4 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 779s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 779s *** Run 76 of 100 779s /usr/bin/bowtie2 --nofw --score-min L,3.44939893493378,4.04575665057139 -i L,0.00794965549172867 -R 1 --rfg 15.2065441382845 --cp-min 2 --large-index --cp-ival 1 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 779s /usr/bin/bowtie2 --nofw --score-min L,3.44939893493378,4.04575665057139 -i L,0.00794965549172867 -R 1 --rfg 15.2065441382845 --cp-min 2 --large-index --cp-ival 1 --qseq -p 4 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 779s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 779s *** Run 77 of 100 779s /usr/bin/bowtie2 --cp-ival 1 -i S,2.17984049175235 -N 0 -L19 --mp 5.79270519613286,2.74121297244127 --trim3 0 --rfg 18.5400746776286,8.1471328812215 --np 1 --cp-min 3 --large-index -R 4 -D 27 --gbar 2 --score-min L,2.91890677861268,6.99514998476382 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 779s /usr/bin/bowtie2 --cp-ival 1 -i S,2.17984049175235 -N 0 -L19 --mp 5.79270519613286,2.74121297244127 --trim3 0 --rfg 18.5400746776286,8.1471328812215 --np 1 --cp-min 3 --large-index -R 4 -D 27 --gbar 2 --score-min L,2.91890677861268,6.99514998476382 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 779s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 779s /usr/bin/bowtie2 --cp-ival 1 -i S,2.17984049175235 -N 0 -L19 --mp 5.79270519613286,2.74121297244127 --trim3 0 --rfg 18.5400746776286,8.1471328812215 --np 1 --cp-min 3 --large-index -R 4 -D 27 --gbar 2 --score-min L,2.91890677861268,6.99514998476382 --qseq -p 3 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 779s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 779s *** Run 78 of 100 779s /usr/bin/bowtie2 --mp 6.74083409317345,1.61500162970048 -D 39 --gbar 1 --trim3 6 --score-min L,1.37329115286923,9.18358837468783 --rfg 12.0648801291896,14.3260282784293 --norc --cp-min 4 --large-index -a --cp-ival 2 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 779s *** Run 79 of 100 779s /usr/bin/bowtie2 -M 8 --cp-ival 1 --trim3 7 --large-index --cp-min 4 --np 2 -D 33 --gbar 2 --score-min L,6.90311480675114,2.13948055396594 --ma 16.6883664822724 --mm -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.1 779s Introducing 9 SNPs, 0/2 ref/read gaps, and 2 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.2 779s Introducing 22 SNPs, 1/1 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 31 779s Reference gaps introduced: 1 779s Read gaps introduced: 3 779s Rearrangements introduced: 2 779s Created read sampler 779s Sampling 57 reads 779s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 779s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 76 reference bases 779s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '0' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '0' because it was < 2 characters long 779s Warning: skipping mate #2 of read '0' because it was < 2 characters long 779s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '2' because it was < 2 characters long 779s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '7' because it was < 2 characters long 779s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '15' because it was < 2 characters long 779s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '16' because it was < 2 characters long 779s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '20' because it was < 2 characters long 779s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '21' because it was < 2 characters long 779s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '24' because it was < 2 characters long 779s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '25' because it was < 2 characters long 779s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '29' because it was < 2 characters long 779s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '30' because it was < 2 characters long 779s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '31' because it was < 2 characters long 779s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '34' because it was < 2 characters long 779s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '36' because it was < 2 characters long 779s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '46' because it was < 2 characters long 779s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '48' because it was < 2 characters long 779s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '52' because it was < 2 characters long 779s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '54' because it was < 2 characters long 779s 57 reads; of these: 779s 43 (75.44%) were paired; of these: 779s 43 (100.00%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 43 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 43 pairs aligned 0 times concordantly or discordantly; of these: 779s 86 mates make up the pairs; of these: 779s 86 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 14 (24.56%) were unpaired; of these: 779s 14 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 0.00% overall alignment rate 779s Read 50 alignments... 779s Read 100 alignments... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 0 alignments, 0 edits 779s --------------- 779s PASSED 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.2 779s Introducing 18 SNPs, 0/0 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.1 779s Introducing 8 SNPs, 1/2 ref/read gaps, and 2 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 26 779s Reference gaps introduced: 1 779s Read gaps introduced: 2 779s Rearrangements introduced: 2 779s Created read sampler 779s Sampling 119 reads 779s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 779s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 76 reference bases 779s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '18' because it was < 2 characters long 779s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '26' because it was < 2 characters long 779s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '27' because it was < 2 characters long 779s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '29' because it was < 2 characters long 779s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '35' because it was < 2 characters long 779s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '40' because it was < 2 characters long 779s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '47' because it was < 2 characters long 779s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '60' because it was < 2 characters long 779s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '65' because it was < 2 characters long 779s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '67' because it was < 2 characters long 779s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '73' because it was < 2 characters long 779s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '79' because it was < 2 characters long 779s Read 50 alignments... 779s Warning: skipping mate #2 of read '104' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '104' because it was < 2 characters long 779s Warning: skipping mate #2 of read '107' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '107' because it was < 2 characters long 779s Read 100 alignments... 779s Read 150 alignments... 779s Warning: skipping mate #1 of read '115' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '115' because it was < 2 characters long 779s 119 reads; of these: 779s 100 (84.03%) were paired; of these: 779s 100 (100.00%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 100 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 100 pairs aligned 0 times concordantly or discordantly; of these: 779s 200 mates make up the pairs; of these: 779s 200 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 19 (15.97%) were unpaired; of these: 779s 19 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 0.00% overall alignment rate 779s Read 200 alignments... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 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line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 0 alignments, 0 edits 779s --------------- 779s PASSED 779s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 779s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '18' because it was < 2 characters long 779s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '26' because it was < 2 characters long 779s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '27' because it was < 2 characters long 779s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '29' because it was < 2 characters long 779s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '35' because it was < 2 characters long 779s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '40' because it was < 2 characters long 779s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '47' because it was < 2 characters long 779s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '60' because it was < 2 characters long 779s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '65' because it was < 2 characters long 779s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '67' because it was < 2 characters long 779s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '73' because it was < 2 characters long 779s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '79' because it was < 2 characters long 779s Warning: skipping mate #2 of read '104' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '104' because it was < 2 characters long 779s Warning: skipping mate #2 of read '107' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '107' because it was < 2 characters long 779s Warning: skipping mate #1 of read '115' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '115' because it was < 2 characters long 779s 119 reads; of these: 779s 100 (84.03%) were paired; of these: 779s 100 (100.00%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 100 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 100 pairs aligned 0 times concordantly or discordantly; of these: 779s 200 mates make up the pairs; of these: 779s 200 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 19 (15.97%) were unpaired; of these: 779s 19 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 0.00% overall alignment rate 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.2 779s Introducing 7 SNPs, 1/2 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.1 779s Introducing 6 SNPs, 2/2 ref/read gaps, and 1 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 13 779s Reference gaps introduced: 3 779s Read gaps introduced: 4 779s Rearrangements introduced: 1 779s Created read sampler 779s Sampling 50 reads 779s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 779s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 76 reference bases 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 779s 50 reads; of these: 779s 50 (100.00%) were unpaired; of these: 779s 46 (92.00%) aligned 0 times 779s 2 (4.00%) aligned exactly 1 time 779s 2 (4.00%) aligned >1 times 779s 8.00% overall alignment rate 779s Read 50 alignments... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GCTGGGGGGTAGGGG 779s GCTGGGGGGTAGGGG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AC 779s AC 779s Processing line... 779s Processing line... 779s CG 779s CG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TC 779s TC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 4 alignments, 0 edits 779s --------------- 779s PASSED 779s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 779s 50 reads; of these: 779s 50 (100.00%) were unpaired; of these: 779s 46 (92.00%) aligned 0 times 779s 2 (4.00%) aligned exactly 1 time 779s 2 (4.00%) aligned >1 times 779s 8.00% overall alignment rate 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.1 779s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.2 779s Introducing 14 SNPs, 0/1 ref/read gaps, and 1 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 14 779s Reference gaps introduced: 0 779s Read gaps introduced: 2 779s Rearrangements introduced: 1 779s Created read sampler 779s Sampling 144 reads 779s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 779s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 76 reference bases 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 779s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 779s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 779s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 779s Read 50 alignments... 779s Read 100 alignments... 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 779s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 779s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 779s Warning: skipping mate #2 of read 'R_1_1_1_118_118_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 779s Read 150 alignments... 779s 144 reads; of these: 779s 144 (100.00%) were paired; of these: 779s 143 (99.31%) aligned concordantly 0 times 779s 1 (0.69%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 143 pairs aligned concordantly 0 times; of these: 779s 1 (0.70%) aligned discordantly 1 time 779s ---- 779s 142 pairs aligned 0 times concordantly or discordantly; of these: 779s 284 mates make up the pairs; of these: 779s 255 (89.79%) aligned 0 times 779s 8 (2.82%) aligned exactly 1 time 779s 21 (7.39%) aligned >1 times 779s 11.46% overall alignment rate 779s Read 200 alignments... 779s Read 250 alignments... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TCG 779s TCG 779s Processing line... 779s Processing line... 779s CC 779s CC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GGT 779s GGT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GGC 779s GGC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AGTT 779s AGTT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GGGTGG 779s GGGTGG 779s Processing line... 779s ACCTG 779s ACCTG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GGTAGGGGCG 779s GGTAGGGGCG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GG 779s GG 779s Processing line... 779s Processing line... 779s TG 779s TG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GGCGATTA 779s GGCGATTA 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GGC 779s GGC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GG 779s GG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GTTG 779s GTTG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TG 779s TG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GGTAGGGGCGATTAG 779s GGTAGGGGCGATTAG 779s Processing line... 779s Processing line... 779s GAG 779s GAG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GGGT 779s GGGT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CTG 779s CTG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CTGGGG 779s CTGGGG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CGG 779s CGG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CTGGGGGGTAGGGGCGATTAGTTG 779s CTGGGGGGTAGGGGCGATTAGTTG 779s Processing line... 779s GGA 779s GGA 779s Processing line... 779s GGGGCGATTAGTTGGAGTTC 779s GGGGCGATTAGTTGGAGTTC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TGGCTGGGGGGTAGGGGCGATTAGTT 779s TGGCTGGGGGGTAGGGGCGATTAGTT 779s Processing line... 779s Processing line... 779s TGC 779s TGC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GGGGGTAGG 779s GGGGGTAGG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CG 779s CG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AT 779s AT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CTGG 779s CTGG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GGG 779s GGG 779s Processing line... 779s Processing line... 779s GGT 779s GGT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GGGTAGGG 779s GGGTAGGG 779s Processing line... 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 33 alignments, 0 edits 779s --------------- 779s PASSED 779s ALSO checking that bowtie2 and bowtie2-align match up 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 779s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 779s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 779s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 779s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 779s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 779s Warning: skipping mate #2 of read 'R_1_1_1_118_118_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 779s 144 reads; of these: 779s 144 (100.00%) were paired; of these: 779s 143 (99.31%) aligned concordantly 0 times 779s 1 (0.69%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 143 pairs aligned concordantly 0 times; of these: 779s 1 (0.70%) aligned discordantly 1 time 779s ---- 779s 142 pairs aligned 0 times concordantly or discordantly; of these: 779s 284 mates make up the pairs; of these: 779s 255 (89.79%) aligned 0 times 779s 8 (2.82%) aligned exactly 1 time 779s 21 (7.39%) aligned >1 times 779s 11.46% overall alignment rate 779s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 779s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 779s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 779s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 779s Warning: skipping mate #2 of read 'R_1_1_1_118_118_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 779s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 779s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 779s 144 reads; of these: 779s 144 (100.00%) were paired; of these: 779s 143 (99.31%) aligned concordantly 0 times 779s 1 (0.69%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 143 pairs aligned concordantly 0 times; of these: 779s 1 (0.70%) aligned discordantly 1 time 779s ---- 779s 142 pairs aligned 0 times concordantly or discordantly; of these: 779s 284 mates make up the pairs; of these: 779s 255 (89.79%) aligned 0 times 779s 8 (2.82%) aligned exactly 1 time 779s 21 (7.39%) aligned >1 times 779s 11.46% overall alignment rate 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.2 779s Introducing 16 SNPs, 0/1 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.1 779s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 23 779s Reference gaps introduced: 1 779s Read gaps introduced: 1 779s Rearrangements introduced: 0 779s Created read sampler 779s Sampling 117 reads 779s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 779s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 76 reference bases 779s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 779s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '2' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 779s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 779s Warning: skipping read '8' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 779s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '20' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 779s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 779s Warning: skipping read '25' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 779s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '38' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 779s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '42' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 779s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '43' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 779s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '47' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 779s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '58' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 779s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 779s Warning: skipping read '88' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 779s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '89' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 779s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '100' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 779s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '112' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 779s Warning: skipping read '113' because length (1) <= # seed mismatches (0) 779s Warning: skipping read '113' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 779s 117 reads; of these: 779s 117 (100.00%) were unpaired; of these: 779s 110 (94.02%) aligned 0 times 779s 6 (5.13%) aligned exactly 1 time 779s 1 (0.85%) aligned >1 times 779s 5.98% overall alignment rate 779s Read 50 alignments... 779s Read 100 alignments... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GATTAGTTGGAG 779s GATTAGTTGGAG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CT 779s CT 779s Processing line... 779s CT 779s CT 779s Processing line... 779s CT 779s CT 779s Processing line... 779s CT 779s CT 779s Processing line... 779s CT 779s CT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TGGCTGGGGGG 779s TGGCTGGGGGG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CTCTCGGTTCGGGGGT 779s CTCTCGGTTCGGGGGT 779s Processing line... 779s Processing line... 779s GGGTT 779s GGGTT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CTCTCGGTTCG 779s CTCTCGGTTCG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TGCTC 779s TGCTC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 11 alignments, 0 edits 779s --------------- 779s PASSED 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.2 779s Introducing 18 SNPs, 0/3 ref/read gaps, and 1 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.1 779s Introducing 4 SNPs, 4/0 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 22 779s Reference gaps introduced: 4 779s Read gaps introduced: 3 779s Rearrangements introduced: 1 779s Created read sampler 779s Sampling 56 reads 779s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 779s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 76 reference bases 779s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 779s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 779s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 779s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '0' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 779s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '4' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 779s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '8' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 779s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '9' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 779s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '13' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 779s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '14' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 779s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '22' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 779s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '24' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 779s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '34' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 779s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '39' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 779s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '45' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 779s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '47' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 779s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '48' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 779s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '49' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 779s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '55' because it was < 2 characters long 779s 56 reads; of these: 779s 56 (100.00%) were unpaired; of these: 779s 50 (89.29%) aligned 0 times 779s 4 (7.14%) aligned exactly 1 time 779s 2 (3.57%) aligned >1 times 779s 10.71% overall alignment rate 779s Read 50 alignments... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GC 779s GC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GCT 779s GCT 779s Processing line... 779s Processing line... 779s Processing line... 779s GGCGATTAG 779s GGCGATTAG 779s Processing line... 779s Processing line... 779s Processing line... 779s GGGGGTAGGGGCGA 779s GGGGGTAGGGGCGA 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GGTGG 779s GGTGG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CGATTAGTTGGA 779s CGATTAGTTGGA 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 6 alignments, 0 edits 779s --------------- 779s PASSED 779s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 779s /usr/bin/bowtie2 -M 8 --cp-ival 1 --trim3 7 --large-index --cp-min 4 --np 2 -D 33 --gbar 2 --score-min L,6.90311480675114,2.13948055396594 --ma 16.6883664822724 --mm -r -p 2 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 779s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 779s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 779s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 779s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '0' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 779s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '4' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 779s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '8' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 779s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '9' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 779s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '13' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 779s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '14' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 779s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '22' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 779s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '24' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 779s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '34' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 779s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '39' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 779s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '45' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 779s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '47' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 779s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '48' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 779s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '49' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 779s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '55' because it was < 2 characters long 779s 56 reads; of these: 779s 56 (100.00%) were unpaired; of these: 779s 50 (89.29%) aligned 0 times 779s 4 (7.14%) aligned exactly 1 time 779s 2 (3.57%) aligned >1 times 779s 10.71% overall alignment rate 779s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.2 779s Introducing 8 SNPs, 2/1 ref/read gaps, and 3 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.1 779s Introducing 8 SNPs, 0/1 ref/read gaps, and 2 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 16 779s Reference gaps introduced: 2 779s Read gaps introduced: 2 779s Rearrangements introduced: 5 779s Created read sampler 779s Sampling 84 reads 779s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 779s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 76 reference bases 779s *** Run 80 of 100 779s /usr/bin/bowtie2 --score-min L,9.92558204507198,1.92219008663025 -i S,2.34435218166091,0.506903506390191 --rfg 1.58945566467183 --large-index --np 3 --cp-min 3 --n-ceil 0.732999076277447,0.72458463701871 --local --cp-ival 2 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 779s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '2' because it was < 2 characters long 779s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '40' because it was < 2 characters long 779s 84 reads; of these: 779s 84 (100.00%) were paired; of these: 779s 84 (100.00%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 84 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 84 pairs aligned 0 times concordantly or discordantly; of these: 779s 168 mates make up the pairs; of these: 779s 168 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 0.00% overall alignment rate 779s Read 50 alignments... 779s Read 100 alignments... 779s Read 150 alignments... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s /usr/bin/bowtie2 --score-min L,9.92558204507198,1.92219008663025 -i S,2.34435218166091,0.506903506390191 --rfg 1.58945566467183 --large-index --np 3 --cp-min 3 --n-ceil 0.732999076277447,0.72458463701871 --local --cp-ival 2 -f -p 2 -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 0 alignments, 0 edits 779s --------------- 779s PASSED 779s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 779s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '2' because it was < 2 characters long 779s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '40' because it was < 2 characters long 779s 84 reads; of these: 779s 84 (100.00%) were paired; of these: 779s 84 (100.00%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 84 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 84 pairs aligned 0 times concordantly or discordantly; of these: 779s 168 mates make up the pairs; of these: 779s 168 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 0.00% overall alignment rate 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 779s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.1 779s Introducing 15 SNPs, 0/0 ref/read gaps, and 1 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.2 779s Introducing 21 SNPs, 2/0 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 36 779s Reference gaps introduced: 2 779s Read gaps introduced: 0 779s Rearrangements introduced: 1 779s Created read sampler 779s Sampling 67 reads 779s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 779s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 76 reference bases 779s *** Run 81 of 100 779s /usr/bin/bowtie2 --mm --rdg 8.65502049060387,7.96699459487318 --gbar 2 --ma 2.80379464306056 --score-min L,3.15524150905922,1.74112377129287 --cp-min 5 --np 5 --large-index --rfg 26.8332968851692,16.1536395442949 --cp-ival 7 --n-ceil 0.691085556401998,0.970809959116786 --trim5 3 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 780s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 780s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '10' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 780s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #2 of read '28' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 780s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '34' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 780s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '40' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 780s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '54' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 780s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '63' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 780s Read 50 alignments... 780s Read 100 alignments... 780s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 780s 67 reads; of these: 780s 59 (88.06%) were paired; of these: 780s 59 (100.00%) aligned concordantly 0 times 780s 0 (0.00%) aligned concordantly exactly 1 time 780s 0 (0.00%) aligned concordantly >1 times 780s ---- 780s 59 pairs aligned concordantly 0 times; of these: 780s 0 (0.00%) aligned discordantly 1 time 780s ---- 780s 59 pairs aligned 0 times concordantly or discordantly; of these: 780s 118 mates make up the pairs; of these: 780s 109 (92.37%) aligned 0 times 780s 7 (5.93%) aligned exactly 1 time 780s 2 (1.69%) aligned >1 times 780s 8 (11.94%) were unpaired; of these: 780s 5 (62.50%) aligned 0 times 780s 1 (12.50%) aligned exactly 1 time 780s 2 (25.00%) aligned >1 times 780s 9.52% overall alignment rate 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s CTC 780s CTC 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GCT 780s GCT 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GCTCTC 780s GCTCTC 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s CTG 780s CTG 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GGGCG 780s GGGCG 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GCTCTCGGTTCGGGGGTGGCTGGGGGGT 780s GCTCTCGGTTCGGGGGTGGCTGGGGGGT 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GTTCTG 780s GTTCTG 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s TTAGTTGGAGTTCT 780s TTAGTTGGAGTTCT 780s Processing line... 780s Processing line... 780s CTGGGGGGT 780s CTGGGGGGT 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s CTGGGGGGTAGGGG 780s CTGGGGGGTAGGGG 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GGA 780s GGA 780s /usr/bin/bowtie2 --mm --rdg 8.65502049060387,7.96699459487318 --gbar 2 --ma 2.80379464306056 --score-min L,3.15524150905922,1.74112377129287 --cp-min 5 --np 5 --large-index --rfg 26.8332968851692,16.1536395442949 --cp-ival 7 --n-ceil 0.691085556401998,0.970809959116786 --trim5 3 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 780s Processing line... 780s GT 780s GT 780s Processing line... 780s Processing line... 780s --- Summary --- 780s Read 1 reference strings 780s Checked 12 alignments, 0 edits 780s --------------- 780s PASSED 780s ALSO checking that bowtie2 and bowtie2-align match up 780s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 780s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '10' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 780s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #2 of read '28' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 780s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '34' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 780s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '40' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 780s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '54' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 780s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '63' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 780s 67diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 780s *** Run 82 of 100 780s /usr/bin/bowtie2 --rdg 22.1391978370174,8.90154574561463 --rfg 13.1347799191514,1.89659692915657 --nofw --trim3 3 --score-min L,1.2918388824008,4.81167729850513 --local --cp-ival 1 --cp-min 2 --large-index --n-ceil 0.81752665037744,0.529573247541546 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 780s reads; of these: 780s 59 (88.06%) were paired; of these: 780s 59 (100.00%) aligned concordantly 0 times 780s 0 (0.00%) aligned concordantly exactly 1 time 780s 0 (0.00%) aligned concordantly >1 times 780s ---- 780s 59 pairs aligned concordantly 0 times; of these: 780s 0 (0.00%) aligned discordantly 1 time 780s ---- 780s 59 pairs aligned 0 times concordantly or discordantly; of these: 780s 118 mates make up the pairs; of these: 780s 109 (92.37%) aligned 0 times 780s 7 (5.93%) aligned exactly 1 time 780s 2 (1.69%) aligned >1 times 780s 8 (11.94%) were unpaired; of these: 780s 5 (62.50%) aligned 0 times 780s 1 (12.50%) aligned exactly 1 time 780s 2 (25.00%) aligned >1 times 780s 9.52% overall alignment rate 780s Flattened IUPAC characters 780s Mutating sequence Sim.pm.1 780s Introducing 20 SNPs, 2/0 ref/read gaps, and 1 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutating sequence Sim.pm.2 780s Introducing 20 SNPs, 0/0 ref/read gaps, and 1 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutated reference genome to subject genome 780s SNPs introduced: 40 780s Reference gaps introduced: 2 780s Read gaps introduced: 0 780s Rearrangements introduced: 2 780s Created read sampler 780s Sampling 86 reads 780s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 780s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 780s parsing sequence Sim.pm.1... 780s parsing sequence Sim.pm.2... 780s Parsed 76 reference bases 780s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '4' because it was < 2 characters long 780s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '10' because it was < 2 characters long 780s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #2 of read '21' because it was < 2 characters long 780s Warning: skipping mate #1 of read '26' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '26' because it was < 2 characters long 780s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '31' because it was < 2 characters long 780s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #2 of read '58' because it was < 2 characters long 780s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '59' because it was < 2 characters long 780s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #2 of read '63' because it was < 2 characters long 780s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '67' because it was < 2 characters long 780s Warning: skipping mate #2 of read '68' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #2 of read '68' because it was < 2 characters long 780s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '70' because it was < 2 characters long 780s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 780s Warning: skipping read '71' because it was < 2 characters long 780s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '79' because it was < 2 characters long 780s Read 50 alignments... 780s 86 reads; of these: 780s 79 (91.86%) were paired; of these: 780s 79 (100.00%) aligned concordantly 0 times 780s 0 (0.00%) aligned concordantly exactly 1 time 780s 0 (0.00%) aligned concordantly >1 times 780s ---- 780s 79 pairs aligned concordantly 0 times; of these: 780s 0 (0.00%) aligned discordantly 1 time 780s ---- 780s 79 pairs aligned 0 times concordantly or discordantly; of these: 780s 158 mates make up the pairs; of these: 780s 158 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 7 (8.14%) were unpaired; of these: 780s 7 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 0.00% overall alignment rate 780s Read 100 alignments... 780s Read 150 alignments... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s --- Summary --- 780s Read 1 reference strings 780s Checked 0 alignments, 0 edits 780s --------------- 780s PASSED 780s Flattened IUPAC characters 780s Mutating sequence Sim.pm.2 780s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutating sequence Sim.pm.1 780s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutated reference genome to subject genome 780s SNPs introduced: 9 780s Reference gaps introduced: 0 780s Read gaps introduced: 0 780s Rearrangements introduced: 0 780s Created read sampler 780s Sampling 123 reads 780s *** Run 83 of 100 780s /usr/bin/bowtie2 --nofw --score-min L,7.40047366313649,9.98630183648116 --mp 9.43874097303161,7.40672652543139 -R 4 --mm --rfg 30.1928378047381 --cp-min 4 --large-index --norc --trim5 1 --local --cp-ival 1 --qseq -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq 780s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 780s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 780s parsing sequence Sim.pm.1... 780s parsing sequence Sim.pm.2... 780s Parsed 76 reference bases 780s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 780s 123 reads; of these: 780s 123 (100.00%) were unpaired; of these: 780s 123 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 0.00% overall alignment rate 780s Read 50 alignments... 780s Read 100 alignments... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s /usr/bin/bowtie2 --nofw --score-min L,7.40047366313649,9.98630183648116 --mp 9.43874097303161,7.40672652543139 -R 4 --mm --rfg 30.1928378047381 --cp-min 4 --large-index --norc --trim5 1 --local --cp-ival 1 --qseq -p 3 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s --- Summary --- 780s Read 1 reference strings 780s Checked 0 alignments, 0 edits 780s --------------- 780s PASSED 780s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 780s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 780s 123 reads; of these: 780s 123 (100.00%) were unpaired; of these: 780s 123 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 0.00% overall alignment rate 780s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 780s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 780s Flattened IUPAC characters 780s Mutating sequence Sim.pm.2 780s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 780s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutating sequence Sim.pm.1 780s Introducing 10 SNPs, 1/3 ref/read gaps, and 1 rearrangements 780s *** Run 84 of 100 780s /usr/bin/bowtie2 --cp-min 3 --np 2 --large-index --mm --score-min L,4.39686136587207,6.16958734086478 --cp-ival 1 --local --trim5 8 -a --rfg 29.5188206127378,11.4239860656852 -N 1 -L22 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutated reference genome to subject genome 780s SNPs introduced: 19 780s Reference gaps introduced: 1 780s Read gaps introduced: 3 780s Rearrangements introduced: 1 780s Created read sampler 780s Sampling 40 reads 780s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 780s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 780s parsing sequence Sim.pm.1... 780s parsing sequence Sim.pm.2... 780s Parsed 76 reference bases 780s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '1' because it was < 2 characters long 781s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '6' because it was < 2 characters long 781s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '14' because it was < 2 characters long 781s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '24' because it was < 2 characters long 781s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '29' because it was < 2 characters long 781s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '37' because it was < 2 characters long 781s 40 reads; of these: 781s 33 (82.50%) were paired; of these: 781s 33 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 33 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 33 pairs aligned 0 times concordantly or discordantly; of these: 781s 66 mates make up the pairs; of these: 781s 66 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 7 (17.50%) were unpaired; of these: 781s 7 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 0.00% overall alignment rate 781s Read 50 alignments... 781s Processing line... 781s Processing line... 781s /usr/bin/bowtie2 --cp-min 3 --np 2 --large-index --mm --score-min L,4.39686136587207,6.16958734086478 --cp-ival 1 --local --trim5 8 -a --rfg 29.5188206127378,11.4239860656852 -N 1 -L22 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s --- Summary --- 781s Read 1 reference strings 781s Checked 0 alignments, 0 edits 781s --------------- 781s PASSED 781s ALSO checking that bowtie2 and bowtie2-align match up 781s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '1' because it was < 2 characters long 781s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '6' because it was < 2 characters long 781s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '14' because it was < 2 characters long 781s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '24' because it was < 2 characters long 781s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '29' because it was < 2 characters long 781s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '37' because it was < 2 characters long 781s 40 reads; of these: 781s 33 (82.50%) were paired; of these: 781s 33 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 33 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 33 pairs aligned 0 times concordantly or discordantly; of these: 781s 66 mates make up the pairs; of these: 781s 66 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 7 (17.50%) were unpaired; of these: 781s 7 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 0.00% overall alignment rate 781s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 781s /usr/bin/bowtie2 --cp-min 3 --np 2 --large-index --mm --score-min L,4.39686136587207,6.16958734086478 --cp-ival 1 --local --trim5 8 -a --rfg 29.5188206127378,11.4239860656852 -N 1 -L22 -q -p 4 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 781s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 781s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '1' because it was < 2 characters long 781s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '6' because it was < 2 characters long 781s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '14' because it was < 2 characters long 781s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '24' because it was < 2 characters long 781s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '29' because it was < 2 characters long 781s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '37' because it was < 2 characters long 781s 40 reads; of these: 781s 33 (82.50%) were paired; of these: 781s 33 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 33 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 timediff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 781s 781s ---- 781s 33 pairs aligned 0 times concordantly or discordantly; of these: 781s 66 mates make up the pairs; of these: 781s 66 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 7 (17.50%) were unpaired; of these: 781s 7 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 0.00% overall alignment rate 781s Flattened IUPAC characters 781s Mutating sequence Sim.pm.2 781s Introducing 7 SNPs, 0/3 ref/read gaps, and 1 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutating sequence Sim.pm.1 781s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutated reference genome to subject genome 781s SNPs introduced: 7 781s Reference gaps introduced: 1 781s Read gaps introduced: 3 781s Rearrangements introduced: 2 781s Created read sampler 781s Sampling 19 reads 781s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 781s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 781s parsing sequence Sim.pm.1... 781s parsing sequence Sim.pm.2... 781s Parsed 76 reference bases 781s *** Run 85 of 100 781s /usr/bin/bowtie2 --mp 9.57845673066044,7.56624432053918 -R 3 --score-min L,6.89666128587733,5.6293816396489 --rfg 33.5202095616692,11.1616815155106 --mm --trim5 0 --large-index --cp-min 10 --cp-ival 2 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 781s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '1' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 781s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '13' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 781s 19 reads; of these: 781s 19 (100.00%) were paired; of these: 781s 19 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 19 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 19 pairs aligned 0 times concordantly or discordantly; of these: 781s 38 mates make up the pairs; of these: 781s 36 (94.74%) aligned 0 times 781s 2 (5.26%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 5.26% overall alignment rate 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s /usr/bin/bowtie2 --mp 9.57845673066044,7.56624432053918 -R 3 --score-min L,6.89666128587733,5.6293816396489 --rfg 33.5202095616692,11.1616815155106 --mm --trim5 0 --large-index --cp-min 10 --cp-ival 2 -q -p 4 -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 781s Processing line... 781s Processing line... 781s CCTG 781s CCTG 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s GGTTACCTGGG 781s GGTTACCTGGG 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s --- Summary --- 781s Read 1 reference strings 781s Checked 2 alignments, 0 edits 781s --------------- 781s PASSED 781s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 781s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '1' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 781s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '13' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 781s 19 reads; of these: 781s 19 (100.00%) were paired; of these: 781s 19 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 19 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 19 pairs aligned 0 times concordantly or discordantly; of these: 781s 38 mates make up the pairs; of these: 781s 36 (94.74%) aligned 0 times 781s 2 (5.26%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 5.26% overall alignment rate 781s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 781s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 781s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 781s /usr/bin/bowtie2 --mp 9.57845673066044,7.56624432053918 -R 3 --score-min L,6.89666128587733,5.6293816396489 --rfg 33.5202095616692,11.1616815155106 --mm --trim5 0 --large-index --cp-min 10 --cp-ival 2 -q -p 2 -x /tmp/Sim.pm.qJbFQMAC --reorder -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 781s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 781s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '1' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 781s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '13' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 781s 19 reads; of these: 781s 19 (100.00%) were paired; of these: 781s 19 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 19 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 19 pairs aligned 0 times concordantly or discordantly; of these: 781s 38 mates make up the pairs; of these: 781s 36 (94.74%) aligned 0 times 781s 2 (5.26%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 5.26% overall alignment rate 781s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 781s Flattened IUPAC characters 781s Mutating sequence Sim.pm.1 781s Introducing 14 SNPs, 1/1 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutating sequence Sim.pm.2 781s Introducing 4 SNPs, 0/2 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutated reference genome to subject genome 781s SNPs introduced: 18 781s Reference gaps introduced: 1 781s Read gaps introduced: 3 781s Rearrangements introduced: 0 781s Created read sampler 781s Sampling 121 reads 781s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 781s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 781s parsing sequence Sim.pm.1... 781s parsing sequence Sim.pm.2... 781s Parsed 76 reference bases 781s *** Run 86 of 100 781s /usr/bin/bowtie2 --score-min L,5.93221864394778,6.56378864819279 --nofw --ma 35.9165661921297 -k 6 -i L,1.40198920814743 --cp-ival 1 --large-index --cp-min 7 --norc --trim5 6 -r -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw 782s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 782s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 782s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '5' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 782s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '6' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 782s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '12' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 782s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '16' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 782s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '24' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 782s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '36' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 782s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '43' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 782s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '49' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 782s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '51' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 782s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '59' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 782s Read 50 alignments... 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 782s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '72' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 782s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '77' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 782s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '79' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 782s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '80' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 782s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '82' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 782s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '83' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 782s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '90' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 782s Warning: skipping mate #2 of read '106' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read '106' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 782s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '110' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 782s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '119' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 782s Read 100 alignments... 782s 121 reads; of these: 782s 96 (79.34%) were paired; of these: 782s 96 (100.00%) aligned concordantly 0 times 782s 0 (0.00%) aligned concordantly exactly 1 time 782s 0 (0.00%) aligned concordantly >1 times 782s ---- 782s 96 pairs aligned concordantly 0 times; of these: 782s 0 (0.00%) aligned discordantly 1 time 782s ---- 782s 96 pairs aligned 0 times concordantly or discordantly; of these: 782s 192 mates make up the pairs; of these: 782s 192 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 25 (20.66%) were unpaired; of these: 782s 25 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 0.00% overall alignment rate 782s Read 150 alignments... 782s Read 200 alignments... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 0 alignments, 0 edits 782s --------------- 782s PASSED 782s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 782s /usr/bin/bowtie2 --score-min L,5.93221864394778,6.56378864819279 --nofw --ma 35.9165661921297 -k 6 -i L,1.40198920814743 --cp-ival 1 --large-index --cp-min 7 --norc --trim5 6 -r -p 4 -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.raw -2 /tmp/Sim.pm.qJbFQMAC_2.raw | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 782s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 782s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 782s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '5' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 782s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '6' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 782s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '12' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 782s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '16' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 782s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '24' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 782s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '36' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 782s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '43' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 782s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '49' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 782s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '51' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 782s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '59' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 782s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '72' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 782s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '77' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 782s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '79' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 782s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '80' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 782s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '82' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 782s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '83' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 782s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '90' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 782s Warning: skipping mate #2 of read '106' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read '106' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 782s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '110' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 782s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '119' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 782s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 782s 121 reads; of these: 782s 96 (79.34%) were paired; of these: 782s 96 (100.00%) aligned concordantly 0 times 782s 0 (0.00%) aligned concordantly exactly 1 time 782s 0 (0.00%) aligned concordantly >1 times 782s ---- 782s 96 pairs aligned concordantly 0 times; of these: 782s 0 (0.00%) aligned discordantly 1 time 782s ---- 782s 96 pairs aligned 0 times concordantly or discordantly; of these: 782s 192 mates make up the pairs; of these: 782s 192 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 25 (20.66%) were unpaired; of these: 782s 25 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 0.00% overall alignment rate 782s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 782s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.1 782s Introducing 3 SNPs, 2/2 ref/read gaps, and 1 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.2 782s Introducing 14 SNPs, 2/2 ref/read gaps, and 2 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 17 782s Reference gaps introduced: 4 782s Read gaps introduced: 4 782s Rearrangements introduced: 3 782s Created read sampler 782s Sampling 129 reads 782s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 782s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 76 reference bases 782s *** Run 87 of 100 782s /usr/bin/bowtie2 --cp-min 4 --large-index --trim5 1 --cp-ival 9 --score-min L,1.05240205137719,5.12998367987974 --mp 2.18757424826911,1.33158417147801 -k 11 --rdg 4.13285977686433 --mm --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 782s Warning: skipping mate #2 of read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 782s Read 50 alignments... 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 782s Read 100 alignments... 782s Read 150 alignments... 782s Read 200 alignments... 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 782s Read 250 alignments... 782s 129 reads; of these: 782s 128 (99.22%) were paired; of these: 782s 126 (98.44%) aligned concordantly 0 times 782s 0 (0.00%) aligned concordantly exactly 1 time 782s 2 (1.56%) aligned concordantly >1 times 782s ---- 782s 126 pairs aligned concordantly 0 times; of these: 782s 0 (0.00%) aligned discordantly 1 time 782s ---- 782s 126 pairs aligned 0 times concordantly or discordantly; of these: 782s 252 mates make up the pairs; of these: 782s 231 (91.67%) aligned 0 times 782s 11 (4.37%) aligned exactly 1 time 782s 10 (3.97%) aligned >1 times 782s 1 (0.78%) were unpaired; of these: 782s 1 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 9.73% overall alignment rate 782s Read 300 alignments... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TGG 782s TGG 782s Processing line... 782s TGG 782s TGG 782s Processing line... 782s TGG 782s TGG 782s Processing line... 782s TGG 782s TGG 782s Processing line... 782s TGG 782s TGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TCGGGGG 782s TCGGGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GC 782s GC 782s Processing line... 782s GC 782s GC 782s Processing line... 782s GC 782s GC 782s Processing line... 782s GC 782s GC 782s Processing line... 782s GC 782s GC 782s Processing line... 782s GC 782s GC 782s Processing line... 782s GC 782s GC 782s Processing line... 782s GC 782s GC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TT 782s TT 782s Processing line... 782s TT 782s TT 782s Processing line... 782s TT 782s TT 782s Processing line... 782s TT 782s TT 782s Processing line... 782s TT 782s TT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CTGGG 782s CTGGG 782s Processing line... 782s CTGGG 782s CTGGG 782s Processing line... 782s Processing line... 782s CGG 782s CGG 782s Processing line... 782s CGG 782s CGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TGCTCTCGGTT 782s TGCTCTCGGTT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GG 782s GG 782s Processing line... 782s GG 782s GG 782s Processing line... 782s GG 782s GG 782s Processing line... 782s GG 782s GG 782s Processing line... 782s GG 782s GG 782s Processing line... 782s GG 782s GG 782s Processing line... 782s GG 782s GG 782s Processing line... 782s GG 782s GG 782s Processing line... 782s GG 782s GG 782s Processing line... 782s GG 782s GG 782s Processing line... 782s GG 782s GG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CTGGGGGG 782s CTGGGGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GCG 782s GCG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGTGGCTGGG 782s GGTGGCTGGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGTGGCTGGG 782s GGTGGCTGGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGTGGCTGGG 782s GGTGGCTGGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGTGGCTGGG 782s GGTGGCTGGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGTGGCTGGG 782s GGTGGCTGGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGTGGCTGGG 782s GGTGGCTGGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GAT 782s GAT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s Processing line... 782s TCG 782s TCG 782s Processing line... 782s CGA 782s CGA 782s Processing line... 782s TCG 782s TCG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TG 782s TG 782s Processing line... 782s TG 782s TG 782s Processing line... 782s TG 782s TG 782s Processing line... 782s TG 782s TG 782s Processing line... 782s TG 782s TG 782s Processing line... 782s TG 782s TG 782s Processing line... 782s TG 782s TG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGC 782s GGGC 782s Processing line... 782s GGGT 782s GGGT 782s Processing line... 782s GGGC 782s GGGC 782s Processing line... 782s GGGT 782s GGGT 782s Processing line... 782s GGGC 782s GGGC 782s Processing line... 782s GGGT 782s GGGT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CGGTT 782s CGGTT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGGGTAGGGGCGAT 782s GGGGGTAGGGGCGAT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CTCTCGGTTCGGGGGTGGCTG 782s CTCTCGGTTCGGGGGTGGCTG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGC 782s GGC 782s Processing line... 782s GGC 782s GGC 782s Processing line... 782s Processing line... 782s TTCT 782s TTCT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TCTC 782s TCTC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CTCGGTTCGGGGGTGGCTGGGGGGT 782s CTCGGTTCGGGGGTGGCTGGGGGGT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 85 alignments, 0 edits 782s --------------- 782s PASSED 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.2 782s Introducing 10 SNPs, 2/1 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.1 782s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 12 782s Reference gaps introduced: 2 782s Read gaps introduced: 2 782s Rearrangements introduced: 1 782s Created read sampler 782s Sampling 64 reads 782s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 782s *** Run 88 of 100 782s /usr/bin/bowtie2 --cp-ival 1 --large-index --cp-min 2 --np 1 --mm --rfg 5.52717200890631,5.54274263797939 --rdg 16.7327477877417,17.7993371360673 -k 3 --mp 6.77371150197716,2.54580566025967 --score-min L,7.9746351385694,6.26257236456436 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 782s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 76 reference bases 782s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 782s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '8' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 782s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '27' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 782s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '56' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 782s 64 reads; of these: 782s 64 (100.00%) were unpaired; of these: 782s 54 (84.38%) aligned 0 times 782s 4 (6.25%) aligned exactly 1 time 782s 6 (9.38%) aligned >1 times 782s 15.62% overall alignment rate 782s Read 50 alignments... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGTGGCTG 782s GGGTGGCTG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TGGCTGGGGGGTAGGGGCGATTAGTTGGAG 782s TGGCTGGGGGGTAGGGGCGATTAGTTGGAG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TGGG 782s TGGG 782s Processing line... 782s TGGG 782s TGGG 782s Processing line... 782s GGTGGCTGG 782s GGTGGCTGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGT 782s GGT 782s Processing line... 782s GGT 782s GGT 782s Processing line... 782s GGT 782s GGT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s ACC 782s ACC 782s Processing line... 782s GGT 782s GGT 782s Processing line... 782s GGT 782s GGT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GCTCTCGGTTCGGGGGTGGCTGG 782s GCTCTCGGTTCGGGGGTGGCTGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GTG 782s GTG 782s Processing line... 782s GTG 782s GTG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGT 782s GGT 782s Processing line... 782s GGT 782s GGT 782s Processing line... 782s GGT 782s GGT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GTG 782s GTG 782s Processing line... 782s GTG 782s GTG 782s --- Summary --- 782s Read 1 reference strings 782s Checked 19 alignments, 0 edits 782s --------------- 782s PASSED 782s ALSO checking that bowtie2 and bowtie2-align match up 782s /usr/bin/bowtie2 --cp-ival 1 --large-index --cp-min 2 --np 1 --mm --rfg 5.52717200890631,5.54274263797939 --rdg 16.7327477877417,17.7993371360673 -k 3 --mp 6.77371150197716,2.54580566025967 --score-min L,7.9746351385694,6.26257236456436 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 782s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 782s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '8' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 782s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '27' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 782s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '56' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 782s 64 reads; of these: 782s 64 (100.00%) were unpaired; of these: 782s 54 (84.38%) aligned 0 times 782s 4 (6.25%) aligned exactly 1 time 782s 6 (9.38%) aligned >1 times 782s 15.62% overall alignment rate 782s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.1 782s Introducing 7 SNPs, 2/0 ref/read gaps, and 0 rearrangements 782s *** Run 89 of 100 782s /usr/bin/bowtie2 --rdg 18.1091694181223,9.80786867005231 --mm --ma 12.5535515290927 --score-min L,3.37678467343873,7.00822611884178 --gbar 7 --cp-min 2 --np 6 --large-index --rfg 15.0147328489704 -i L,0.210273312578551 --mp 5.87189281876706,1.77471496204416 --cp-ival 1 -M 7 --trim5 5 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.2 782s Introducing 6 SNPs, 0/2 ref/read gaps, and 1 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 13 782s Reference gaps introduced: 2 782s Read gaps introduced: 2 782s Rearrangements introduced: 1 782s Created read sampler 782s Sampling 89 reads 782s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 782s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 76 reference bases 782s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 782s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 782s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 782s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 782s 89 reads; of these: 782s 75 (84.27%) were paired; of these: 782s 73 (97.33%) aligned concordantly 0 times 782s 0 (0.00%) aligned concordantly exactly 1 time 782s 2 (2.67%) aligned concordantly >1 times 782s ---- 782s 73 pairs aligned concordantly 0 times; of these: 782s 0 (0.00%) aligned discordantly 1 time 782s ---- 782s 73 pairs aligned 0 times concordantly or discordantly; of these: 782s 146 mates make up the pairs; of these: 782s 120 (82.19%) aligned 0 times 782s 11 (7.53%) aligned exactly 1 time 782s 15 (10.27%) aligned >1 times 782s 14 (15.73%) were unpaired; of these: 782s 13 (92.86%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 1 (7.14%) aligned >1 times 782s 18.90% overall alignment rate 782s Read 50 alignments... 782s Read 100 alignments... 782s Read 150 alignments... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGG 782s GGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGG 782s GGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGT 782s GGT 782s Processing line... 782s Processing line... 782s Processing line... 782s GGC 782s GGC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s ATTAGTTGGAGTTC 782s ATTAGTTGGAGTTC 782s Processing line... 782s Processing line... 782s Processing line... 782s AG 782s AG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TCG 782s TCG 782s Processing line... 782s Processing line... 782s ACCTGG 782s ACCTGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GTTCGGGGGT 782s GTTCGGGGGT 782s Processing line... 782s Processing line... 782s CTC 782s CTC 782s Processing line... 782s Processing line... 782s Processing line... 782s CGGTTCGGGGGTGGCTGGGGGGTAGG 782s CGGTTCGGGGGTGGCTGGGGGGTAGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CGGG 782s CGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CGGTTCGGGGGTGGCTGGGGGG 782s CGGTTCGGGGGTGGCTGGGGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s CTGG 782s CTGG 782s Processing line... 782s TGGG 782s TGGG 782s Processing line... 782s Processing line... 782s GGGGG 782s GGGGG 782s Processing line... 782s GGGGGGTAGGGGCGAT 782s GGGGGGTAGGGGCGAT 782s Processing line... 782s Processing line... 782s Processing line... 782s AGG 782s AGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGTAGG 782s GGGTAGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GC 782s GC 782s Processing line... 782s CT 782s CT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGGTGGCTGGGGGGTAG 782s GGGGTGGCTGGGGGGTAG 782s Processing line... 782s Processing line... 782s TGCTCTCGGTTCGGGGGTGGCTGGGGGGTA 782s TGCTCTCGGTTCGGGGGTGGCTGGGGGGTA 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGG 782s GGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGC 782s GGC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s AT 782s AT 782s Processing line... 782s Processing line... 782s CGATTAGTTGGAGTTC 782s CGATTAGTTGGAGTTC 782s Processing line... 782s GG 782s GG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGGG 782s GGGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGTGC 782s GGTGC 782s Processing line... 782s Processing line... 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 31 alignments, 0 edits 782s --------------- 782s PASSED 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.2 782s Introducing 14 SNPs, 0/0 ref/read gaps, and 1 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.1 782s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 22 782s Reference gaps introduced: 1 782s Read gaps introduced: 0 782s Rearrangements introduced: 1 782s Created read sampler 782s Sampling 141 reads 782s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.qseq & /tmp/Sim.pm.qJbFQMAC_2.qseq 782s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 76 reference bases 782s *** Run 90 of 100 782s /usr/bin/bowtie2 --large-index --cp-min 3 --np 6 --mm --gbar 2 --score-min L,4.62212705932595,1.73183236839518 --cp-ival 1 --trim5 1 --n-ceil 0.890864414034167,0.121885488908862 -M 5 --rfg 19.1688209764426 -N 0 -L15 --trim3 3 --qseq -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.qseq -2 /tmp/Sim.pm.qJbFQMAC_2.qseq 782s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 782s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 782s Read 50 alignments... 782s Read 100 alignments... 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 782s Warning: skipping mate #2 of read 'R_1_1_1_88_88_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 782s Warning: skipping mate #2 of read 'R_1_1_1_95_95_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 782s Read 150 alignments... 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 782s Read 200 alignments... 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 782s Warning: skipping mate #1 of read 'R_1_1_1_141_141_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 782s 141 reads; of these: 782s 125 (88.65%) were paired; of these: 782s 125 (100.00%) aligned concordantly 0 times 782s 0 (0.00%) aligned concordantly exactly 1 time 782s 0 (0.00%) aligned concordantly >1 times 782s ---- 782s 125 pairs aligned concordantly 0 times; of these: 782s 0 (0.00%) aligned discordantly 1 time 782s ---- 782s 125 pairs aligned 0 times concordantly or discordantly; of these: 782s 250 mates make up the pairs; of these: 782s 231 (92.40%) aligned 0 times 782s 11 (4.40%) aligned exactly 1 time 782s 8 (3.20%) aligned >1 times 782s 16 (11.35%) were unpaired; of these: 782s 14 (87.50%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 2 (12.50%) aligned >1 times 782s 7.89% overall alignment rate 782s Read 250 alignments... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGG 782s GGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GAGTTCTG 782s GAGTTCTG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGGTAG 782s GGGGTAG 782s Processing line... 782s Processing line... 782s Processing line... 782s GA 782s GA 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s AGTTCT 782s AGTTCT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CTCGGT 782s CTCGGT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGGG 782s GGGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGTTC 782s GGTTC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GCTCTCGGTTCGGGGGTG 782s GCTCTCGGTTCGGGGGTG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TACCT 782s TACCT 782s Processing line... 782s Processing line... 782s CT 782s CT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TGGGGGGTAGG 782s TGGGGGGTAGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TGC 782s TGC 782s Processing line... 782s Processing line... 782s GTAGGGGCGATTAG 782s GTAGGGGCGATTAG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s Processing line... 782s Processing line... 782s CG 782s CG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGGCG 782s GGGGCG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GT 782s GT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CTG 782s CTG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GT 782s GT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GTAGGGGCGA 782s GTAGGGGCGA 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 21 alignments, 0 edits 782s --------------- 782s PASSED 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.1 782s Introducing 19 SNPs, 2/0 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.2 782s Introducing 18 SNPs, 2/1 ref/read gaps, and 0 rearrangements 782s *** Run 91 of 100 782s /usr/bin/bowtie2 --cp-min 5 --np 4 --large-index --score-min L,2.34698946983279,8.1717859118254 -R 1 --rdg 13.2761969638414 -a --local --cp-ival 3 --trim3 2 -N 0 -L12 -i L,0.318954702285654,1.43782717465205 --mp 4.43096525251495,1.67122614339656 --rfg 35.0831487751881 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 37 782s Reference gaps introduced: 4 782s Read gaps introduced: 1 782s Rearrangements introduced: 0 782s Created read sampler 782s Sampling 38 reads 782s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 782s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 76 reference bases 782s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '6' because it was < 2 characters long 782s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '16' because it was < 2 characters long 782s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read '30' because it was < 2 characters long 782s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '32' because it was < 2 characters long 782s 38 reads; of these: 782s 34 (89.47%) were paired; of these: 782s 34 (100.00%) aligned concordantly 0 times 782s 0 (0.00%) aligned concordantly exactly 1 time 782s 0 (0.00%) aligned concordantly >1 times 782s ---- 782s 34 pairs aligned concordantly 0 times; of these: 782s 0 (0.00%) aligned discordantly 1 time 782s ---- 782s 34 pairs aligned 0 times concordantly or discordantly; of these: 782s 68 mates make up the pairs; of these: 782s 68 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 4 (10.53%) were unpaired; of these: 782s 4 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 0.00% overall alignment rate 782s Read 50 alignments... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 0 alignments, 0 edits 782s --------------- 782s PASSED 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.2 782s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.1 782s Introducing 12 SNPs, 0/0 ref/read gaps, and 3 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 13 782s Reference gaps introduced: 1 782s Read gaps introduced: 0 782s Rearrangements introduced: 3 782s Created read sampler 782s Sampling 162 reads 782s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 782s *** Run 92 of 100 782s /usr/bin/bowtie2 --score-min L,8.7305217679098,9.62629403929924 --ma 33.4897587516482 --rdg 13.0032863231745 --trim5 8 --large-index --cp-min 2 --np 1 --cp-ival 1 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 782s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 76 reference bases 782s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 782s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 782s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '7' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 782s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '8' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 782s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '22' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 782s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '29' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 782s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '31' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 782s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '38' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 782s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '42' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 782s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '48' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 782s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '54' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 782s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '59' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 782s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '66' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 782s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '68' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 782s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '72' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 782s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '75' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 782s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '78' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 782s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '79' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 782s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '93' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 782s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '94' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 782s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '96' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 782s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '101' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 782s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '110' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 782s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '114' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 782s Warning: skipping read '119' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '119' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 782s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '120' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 782s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '127' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 782s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '129' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 782s Warning: skipping read '139' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '139' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 782s Warning: skipping read '141' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '141' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 782s Warning: skipping read '153' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '153' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 782s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '156' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 782s Read 50 alignments... 782s Read 100 alignments... 782s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 782s Warning: skipping read '161' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '161' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 782s Warning: skipping read '162' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '162' because it was < 2 characters long 782s 162 reads; of these: 782s 162 (100.00%) were unpaired; of these: 782s 132 (81.48%) aligned 0 times 782s 20 (12.35%) aligned exactly 1 time 782s 10 (6.17%) aligned >1 times 782s 18.52% overall alignment rate 782s Read 150 alignments... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TCGGTTCGGGGG 782s TCGGTTCGGGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GTTG 782s GTTG 782s Processing line... 782s CGG 782s CGG 782s Processing line... 782s GGA 782s GGA 782s Processing line... 782s Processing line... 782s Processing line... 782s ACCTGGGG 782s ACCTGGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s /usr/bin/bowtie2 --score-min L,8.7305217679098,9.62629403929924 --ma 33.4897587516482 --rdg 13.0032863231745 --trim5 8 --large-index --cp-min 2 --np 1 --cp-ival 1 -f -p 4 -x /tmp/Sim.pm.qJbFQMAC --reorder /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.reord.als 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGGTGGCTGGGGG 782s GGGGTGGCTGGGGG 782s Processing line... 782s Processing line... 782s GTAG 782s GTAG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GG 782s GG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s ACCTGGGG 782s ACCTGGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TGG 782s TGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GTAGGGGCGATTA 782s GTAGGGGCGATTA 782s Processing line... 782s Processing line... 782s Processing line... 782s CGGGGGTGG 782s CGGGGGTGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TA 782s TA 782s Processing line... 782s GGGGTGGCTGGGGGG 782s GGGGTGGCTGGGGGG 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s Processing line... 782s Processing line... 782s GGCTGGGGGGTAGGGGCGATTA 782s GGCTGGGGGGTAGGGGCGATTA 782s Processing line... 782s TTC 782s TTC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGG 782s GGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GTTGGAGTT 782s GTTGGAGTT 782s Processing line... 782s Processing line... 782s TCTCGGTTCG 782s TCTCGGTTCG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s AGGG 782s AGGG 782s Processing line... 782s GCTG 782s GCTG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GTGG 782s GTGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CTGG 782s CTGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGGCGATTA 782s GGGGCGATTA 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TGGAGTT 782s TGGAGTT 782s Processing line... 782s Processing line... 782s Processing line... 782s TC 782s TC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGGGTGGCTGGGGGG 782s GGGGGTGGCTGGGGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TTG 782s TTG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 30 alignments, 0 edits 782s --------------- 782s PASSED 782s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 783s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 783s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 783s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '7' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 783s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '8' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 783s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '22' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 783s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '29' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 783s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '31' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 783s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '38' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 783s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '42' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 783s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '48' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 783s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '54' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 783s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '59' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 783s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '66' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 783s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '68' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 783s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '72' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 783s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '75' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 783s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '78' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 783s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '79' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 783s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '101' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 783s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '110' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 783s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '114' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 783s Warning: skipping read '119' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '119' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 783s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '120' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 783s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '127' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 783s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '129' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 783s Warning: skipping read '139' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '139' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 783s Warning: skipping read '141' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '141' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 783s Warning: skipping read '153' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '153' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 783s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '156' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 783s Warning: skipping read '161' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '161' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 783s Warning: skipping read '162' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '162' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 783s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '93' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 783s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '94' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 783s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '96' because it was < 2 characters long 783s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als /tmp/Sim.pm.qJbFQMAC.px.reord.als 783s 162 reads; of these: 783s 162 (100.00%) were unpaired; of these: 783s 132 (81.48%) aligned 0 times 783s 20 (12.35%) aligned exactly 1 time 783s 10 (6.17%) aligned >1 times 783s 18.52% overall alignment rate 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.2 783s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.1 783s Introducing 10 SNPs, 1/1 ref/read gaps, and 1 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 17 783s Reference gaps introduced: 1 783s Read gaps introduced: 2 783s Rearrangements introduced: 1 783s Created read sampler 783s Sampling 107 reads 783s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.raw & /tmp/Sim.pm.qJbFQMAC_2.raw 783s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 76 reference bases 783s *** Run 93 of 100 783s /usr/bin/bowtie2 --mp 7.66558264688334,2.98632880292737 -k 3 --score-min L,8.75468940667277,5.79626621849958 --rfg 35.4317300048177 --n-ceil 0.444611673844975,0.260212447549244 --norc --cp-min 7 --large-index --cp-ival 1 --local -r -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.raw 783s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '17' because it was < 2 characters long 783s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '30' because it was < 2 characters long 783s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '54' because it was < 2 characters long 783s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '82' because it was < 2 characters long 783s 107 reads; of these: 783s 107 (100.00%) were unpaired; of these: 783s 107 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 0.00% overall alignment rate 783s Read 50 alignments... 783s Read 100 alignments... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s --- Summary --- 783s Read 1 reference strings 783s Checked 0 alignments, 0 edits 783s --------------- 783s PASSED 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.2 783s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.1 783s Introducing 4 SNPs, 0/2 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 4 783s Reference gaps introduced: 0 783s Read gaps introduced: 2 783s Rearrangements introduced: 1 783s Created read sampler 783s Sampling 28 reads 783s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 783s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 76 reference bases 783s *** Run 94 of 100 783s /usr/bin/bowtie2 --cp-ival 1 --norc --large-index --np 6 --cp-min 2 --mm --score-min L,1.01087780805519,8.60553169458648 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 783s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 783s 28 reads; of these: 783s 28 (100.00%) were unpaired; of these: 783s 27 (96.43%) aligned 0 times 783s 1 (3.57%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 3.57% overall alignment rate 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GGTGGCTGGGGGGTAGGGGCGATTAGTTGGA 783s GGTGGCTGGGGGGTAGGGGCGATTAGTTGGA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s --- Summary --- 783s Read 1 reference strings 783s Checked 1 alignments, 0 edits 783s --------------- 783s PASSED 783s ALSO checking that bowtie2 and bowtie2-align match up 783s /usr/bin/bowtie2 --cp-ival 1 --norc --large-index --np 6 --cp-min 2 --mm --score-min L,1.01087780805519,8.60553169458648 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 783s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 783s 28 reads; of these: 783s 28 (100.00%) were unpaired; of these: 783s 27 (96.43%) aligned 0 times 783s 1 (3.57%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 3.57% overall alignment rate 783s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.2 783s Introducing 9 SNPs, 1/2 ref/read gaps, and 2 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.1 783s Introducing 22 SNPs, 2/0 ref/read gaps, and 2 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 31 783s Reference gaps introduced: 3 783s Read gaps introduced: 2 783s Rearrangements introduced: 4 783s Created read sampler 783s Sampling 120 reads 783s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 783s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 76 reference bases 783s *** Run 95 of 100 783s /usr/bin/bowtie2 --score-min L,6.90648830917268,9.06223501651081 --gbar 2 --mm --np 4 --cp-min 2 --large-index --nofw --trim3 6 --mp 9.85606907110935,7.18172621142433 -N 1 -L15 --rfg 8.25170836336688 --trim5 3 --cp-ival 1 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 783s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 783s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 783s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '12' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 783s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '15' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 783s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '19' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 783s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '30' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 783s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '32' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 783s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '34' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 783s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '40' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 783s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '41' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 783s Warning: skipping read '44' because length (1) <= # seed mismatches (1) 783s Warning: skipping read '44' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 783s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '45' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 783s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '49' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 783s Warning: skipping read '51' because length (1) <= # seed mismatches (1) 783s Warning: skipping read '51' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 783s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '58' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 783s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '59' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 783s Warning: skipping read '60' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '60' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 783s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '68' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 783s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '77' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 783s Warning: skipping read '85' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '85' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 783s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '88' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 783s Warning: skipping read '91' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '91' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 783s Warning: skipping read '96' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '96' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 783s Warning: skipping read '108' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '108' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 783s Warning: skipping read '109' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '109' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 783s Warning: skipping read '112' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '112' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 783s Warning: skipping read '114' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '114' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 783s Warning: skipping read '119' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '119' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 783s Warning: skipping read '120' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '120' because it was < 2 characters long 783s 120 reads; of these: 783s 120 (100.00%) were unpaired; of these: 783s 111 (92.50%) aligned 0 times 783s 7 (5.83%) aligned exactly 1 time 783s 2 (1.67%) aligned >1 times 783s 7.50% overall alignment rate 783s Read 50 alignments... 783s Read 100 alignments... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s ATTAGTTGGA 783s ATTAGTTGGA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s ATTAGTTGGA 783s ATTAGTTGGA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GTTCGGGGGTGGCTGGG 783s GTTCGGGGGTGGCTGGG 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TGCTCT 783s TGCTCT 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GTTCGGGGGTGGCTGGG 783s GTTCGGGGGTGGCTGGG 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s ATTAGTTGGA 783s ATTAGTTGGA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GTG 783s GTG 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GC 783s GC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s CTGGGGGG 783s CTGGGGGG 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s --- Summary --- 783s Read 1 reference strings 783s Checked 9 alignments, 0 edits 783s --------------- 783s PASSED 783s ALSO checking that bowtie2 and bowtie2-align match up 783s /usr/bin/bowtie2 --score-min L,6.90648830917268,9.06223501651081 --gbar 2 --mm --np 4 --cp-min 2 --large-index --nofw --trim3 6 --mp 9.85606907110935,7.18172621142433 -N 1 -L15 --rfg 8.25170836336688 --trim5 3 --cp-ival 1 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 783s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 783s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 783s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '12' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 783s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '15' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 783s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '19' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 783s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '30' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 783s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '32' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 783s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '34' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 783s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '40' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 783s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '41' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 783s Warning: skipping read '44' because length (1) <= # seed mismatches (1) 783s Warning: skipping read '44' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 783s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '45' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 783s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '49' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 783s Warning: skipping read '51' because length (1) <= # seed mismatches (1) 783s Warning: skipping read '51' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 783s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '58' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 783s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '59' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 783s Warning: skipping read '60' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '60' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 783s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '68' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 783s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '77' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 783s Warning: skipping read '85' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '85' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 783s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '88' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 783s Warning: skipping read '91' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '91' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 783s Warning: skipping read '96' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '96' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 783s Warning: skipping read '108' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '108' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 783s Warning: skipping read '109' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '109' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 783s Warning: skipping read '112' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '112' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 783s Warning: skipping read '114' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '114' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 783s Warning: skipping read '119' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '119' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 783s Warning: skipping read '120' because length (0) <= # seed mismatches (1) 783s Warning: skipping read '120' because it was < 2 characters long 783s 120 reads; of these: 783s 120 (100.00%) were unpaired; of these: 783s 111 (92.50%) aligned 0 times 783s 7 (5.83%) aligned exactly 1 time 783s 2 (1.67%) aligned >1 times 783s 7.50% overall alignment rate 783s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.1 783s Introducing 10 SNPs, 0/1 ref/read gaps, and 1 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.2 783s Introducing 7 SNPs, 1/2 ref/read gaps, and 1 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 17 783s Reference gaps introduced: 1 783s Read gaps introduced: 3 783s Rearrangements introduced: 2 783s Created read sampler 783s Sampling 63 reads 783s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 783s *** Run 96 of 100 783s /usr/bin/bowtie2 --rdg 21.5343273959206,8.00722598499349 --score-min L,3.20213886265727,4.13760495823641 --trim3 1 -k 4 --mp 9.61332562106321,8.55486928213569 --local --cp-ival 3 --large-index --cp-min 3 --n-ceil 0.122964393557968,0.360752364464081 --norc -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 783s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 76 reference bases 783s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read '34' because it was < 2 characters long 783s 63 reads; of these: 783s 61 (96.83%) were paired; of these: 783s 61 (100.00%) aligned concordantly 0 times 783s 0 (0.00%) aligned concordantly exactly 1 time 783s 0 (0.00%) aligned concordantly >1 times 783s ---- 783s 61 pairs aligned concordantly 0 times; of these: 783s 0 (0.00%) aligned discordantly 1 time 783s ---- 783s 61 pairs aligned 0 times concordantly or discordantly; of these: 783s 122 mates make up the pairs; of these: 783s 122 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 2 (3.17%) were unpaired; of these: 783s 2 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 0.00% overall alignment rate 783s Read 50 alignments... 783s Read 100 alignments... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s --- Summary --- 783s Read 1 reference strings 783s Checked 0 alignments, 0 edits 783s --------------- 783s PASSED 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.2 783s Introducing 3 SNPs, 1/0 ref/read gaps, and 4 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.1 783s Introducing 11 SNPs, 1/0 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 14 783s Reference gaps introduced: 2 783s Read gaps introduced: 0 783s Rearrangements introduced: 4 783s Created read sampler 783s Sampling 121 reads 783s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 783s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 76 reference bases 783s *** Run 97 of 100 783s /usr/bin/bowtie2 -M 5 --large-index --cp-min 3 --np 2 --cp-ival 1 --local --score-min L,3.12664863176883,3.78622394186865 -q -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq 783s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 783s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '2' because it was < 2 characters long 783s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '12' because it was < 2 characters long 783s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '23' because it was < 2 characters long 783s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '28' because it was < 2 characters long 783s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '31' because it was < 2 characters long 783s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '39' because it was < 2 characters long 783s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '78' because it was < 2 characters long 783s Warning: skipping read '98' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '98' because it was < 2 characters long 783s Warning: skipping read '107' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '107' because it was < 2 characters long 783s 121 reads; of these: 783s 121 (100.00%) were unpaired; of these: 783s 121 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 0.00% overall alignment rate 783s Read 50 alignments... 783s Read 100 alignments... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s /usr/bin/bowtie2 -M 5 --large-index --cp-min 3 --np 2 --cp-ival 1 --local --score-min L,3.12664863176883,3.78622394186865 -q -p 4 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s --- Summary --- 783s Read 1 reference strings 783s Checked 0 alignments, 0 edits 783s --------------- 783s PASSED 783s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 783s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 783s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '2' because it was < 2 characters long 783s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '12' because it was < 2 characters long 783s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '23' because it was < 2 characters long 783s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '28' because it was < 2 characters long 783s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '31' because it was < 2 characters long 783s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '39' because it was < 2 characters long 783s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '78' because it was < 2 characters long 783s Warning: skipping read '98' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '98' because it was < 2 characters long 783s Warning: skipping read '107' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '107' because it was < 2 characters long 783s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 783s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 783s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 783s 121 reads; of these: 783s 121 (100.00%) were unpaired; of these: 783s 121 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 0.00% overall alignment rate 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.1 783s Introducing 0 SNPs, 1/1 ref/read gaps, and 1 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.2 783s Introducing 16 SNPs, 4/2 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 16 783s Reference gaps introduced: 5 783s Read gaps introduced: 3 783s Rearrangements introduced: 1 783s Created read sampler 783s Sampling 95 reads 783s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 783s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 76 reference bases 783s *** Run 98 of 100 783s /usr/bin/bowtie2 --cp-ival 1 --local --trim5 7 --large-index --cp-min 8 -N 0 -L29 --score-min L,6.50297287979755,1.03703821923037 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta 784s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '2' because it was < 2 characters long 784s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '15' because it was < 2 characters long 784s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '24' because it was < 2 characters long 784s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '26' because it was < 2 characters long 784s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '37' because it was < 2 characters long 784s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '43' because it was < 2 characters long 784s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '48' because it was < 2 characters long 784s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '54' because it was < 2 characters long 784s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '59' because it was < 2 characters long 784s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '60' because it was < 2 characters long 784s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '66' because it was < 2 characters long 784s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '74' because it was < 2 characters long 784s Read 50 alignments... 784s Read 100 alignments... 784s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '82' because it was < 2 characters long 784s 95 reads; of these: 784s 81 (85.26%) were paired; of these: 784s 81 (100.00%) aligned concordantly 0 times 784s 0 (0.00%) aligned concordantly exactly 1 time 784s 0 (0.00%) aligned concordantly >1 times 784s ---- 784s 81 pairs aligned concordantly 0 times; of these: 784s 1 (1.23%) aligned discordantly 1 time 784s ---- 784s 80 pairs aligned 0 times concordantly or discordantly; of these: 784s 160 mates make up the pairs; of these: 784s 157 (98.12%) aligned 0 times 784s 3 (1.88%) aligned exactly 1 time 784s 0 (0.00%) aligned >1 times 784s 14 (14.74%) were unpaired; of these: 784s 13 (92.86%) aligned 0 times 784s 1 (7.14%) aligned exactly 1 time 784s 0 (0.00%) aligned >1 times 784s 3.41% overall alignment rate 784s Read 150 alignments... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AGGGGCGATTA 784s AGGGGCGATTA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s /usr/bin/bowtie2 --cp-ival 1 --local --trim5 7 --large-index --cp-min 8 -N 0 -L29 --score-min L,6.50297287979755,1.03703821923037 -f -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fasta -2 /tmp/Sim.pm.qJbFQMAC_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.als 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s TCGGTTCGGGGCTGGCTGGGGGGTAGGG 784s TCGGTTCGGGGGTGGCTGGGGGGTAGGG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GTTGGAGTTC 784s GTTGGAGTTC 784s Processing line... 784s GTAGGGGCGATT 784s GTAGGGGCGATT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GAGTTCT 784s GAGTTCT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CGGTTCGGGGCTGGCTGGGGGGTAGGG 784s CGGTTCGGGGGTGGCTGGGGGGTAGGG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s --- Summary --- 784s Read 1 reference strings 784s Checked 6 alignments, 0 edits 784s --------------- 784s PASSED 784s ALSO checking that bowtie2 and bowtie2-align match up 784s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '2' because it was < 2 characters long 784s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '15' because it was < 2 characters long 784s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '24' because it was < 2 characters long 784s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '26' because it was < 2 characters long 784s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '37' because it was < 2 characters long 784s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '43' because it was < 2 characters long 784s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '48' because it was < 2 characters long 784s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '54' because it was < 2 characters long 784s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '59' because it was < 2 characters long 784s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '60' because it was < 2 characters long 784s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '66' because it was < 2 characters long 784s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '74' because it was < 2 characters long 784s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '82' because it was < 2 characters long 784s 95 reads; of these: 784s 81 (85.26%) were paired; of these: 784s 81 (100.00%) aligned concordantly 0 times 784s 0 (0.00%) aligned concordantly exactly 1 time 784s 0 (0.00%) aligned concordantly >1 times 784s ---- 784s 81 pairs aligned concordantly 0 times; of these: 784s 1 (1.23%) aligned discordantly 1 time 784s ---- 784s 80 pairs aligned 0 times concordantly or discordantly; of these: 784s 160 mates make up the pairs; of these: 784s 157 (98.12%) aligned 0 times 784s 3 (1.88%) aligned exactly 1 time 784s 0 (0.00%) aligned >1 times 784s 14 (14.74%) were unpaired; of these: 784s 13 (92.86%) aligned 0 times 784s 1 (7.14%) aligned exactly 1 time 784s 0 (0.00%) aligned >1 times 784s 3.41% overall alignment rate 784s diff -uw /tmp/Sim.pm.qJbFQMAC.als /tmp/Sim.pm.qJbFQMAC.debug.als 784s Flattened IUPAC characters 784s Mutating sequence Sim.pm.1 784s Introducing 9 SNPs, 0/3 ref/read gaps, and 0 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutating sequence Sim.pm.2 784s Introducing 8 SNPs, 3/1 ref/read gaps, and 0 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutated reference genome to subject genome 784s SNPs introduced: 17 784s Reference gaps introduced: 3 784s Read gaps introduced: 4 784s Rearrangements introduced: 0 784s Created read sampler 784s Sampling 78 reads 784s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fasta & /tmp/Sim.pm.qJbFQMAC_2.fasta 784s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 784s parsing sequence Sim.pm.1... 784s parsing sequence Sim.pm.2... 784s Parsed 76 reference bases 784s *** Run 99 of 100 784s /usr/bin/bowtie2 --cp-min 2 --np 1 --large-index --mm --score-min L,7.44828757788262,6.34735927056779 -R 1 --cp-ival 1 --n-ceil 1.02626534725193,0.831094328613495 --trim5 7 --rfg 38.9557502722548,10.5350122603011 --trim3 2 -N 1 -L15 -i C,1.32413787653284 --mp 9.19922049899294,3.38240932463891 -f -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta 784s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 784s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '8' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 784s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '9' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 784s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '11' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 784s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '12' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 784s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '17' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 784s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '26' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 784s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '31' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 784s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '34' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 784s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '37' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 784s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '47' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 784s Warning: skipping read '50' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '50' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 784s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '51' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 784s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '52' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 784s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '55' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 784s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '57' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 784s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '59' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 784s Warning: skipping read '65' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '65' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 784s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '73' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 784s Warning: skipping read '76' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '76' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 784s Warning: skipping read '78' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '78' because it was < 2 characters long 784s 78 reads; of these: 784s 78 (100.00%) were unpaired; of these: 784s 67 (85.90%) aligned 0 times 784s 8 (10.26%) aligned exactly 1 time 784s 3 (3.85%) aligned >1 times 784s 14.10% overall alignment rate 784s Read 50 alignments... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s TCTCG 784s TCTCG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CG 784s CG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GCTGGG 784s GCTGGG 784s Processing line... 784s Processing line... 784s GGGGTGGCT 784s GGGGTGGCT 784s Processing line... 784s TTGGAG 784s TTGGAG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GGG 784s GGG 784s Processing line... 784s Processing line... 784s Processing line... 784s GGGGCGA 784s GGGGCGA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GGA 784s GGA 784s Processing line... 784s Processing line... 784s GGG 784s GGG 784s Processing line... 784s Processing line... 784s GCTCT 784s GCTCT 784s Processing line... 784s Processing line... 784s Processing line... 784s TTAGTT 784s TTAGTT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s --- Summary --- 784s Read 1 reference strings 784s Checked 11 alignments, 0 edits 784s --------------- 784s PASSED 784s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 784s /usr/bin/bowtie2 --cp-min 2 --np 1 --large-index --mm --score-min L,7.44828757788262,6.34735927056779 -R 1 --cp-ival 1 --n-ceil 1.02626534725193,0.831094328613495 --trim5 7 --rfg 38.9557502722548,10.5350122603011 --trim3 2 -N 1 -L15 -i C,1.32413787653284 --mp 9.19922049899294,3.38240932463891 -f -p 4 -x /tmp/Sim.pm.qJbFQMAC /tmp/Sim.pm.qJbFQMAC_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als 784s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 784s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '8' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 784s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '9' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 784s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '11' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 784s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '12' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 784s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '17' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 784s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '34' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 784s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '37' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 784s Warning: skipping read '50' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '50' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 784s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '51' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 784s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '52' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 784s Warning: skipping read '55' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '55' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 784s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '57' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 784s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '59' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 784s Warning: skipping read '65' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '65' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 784s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '47' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 784s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '26' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 784s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '31' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 784s Warning: skipping read '73' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '73' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 784s Warning: skipping read '76' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '76' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 784s Warning: skipping read '78' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '78' because it was < 2 characters long 784s 78 reads; of these: 784s 78 (100.00%) were unpaired; of these: 784s 67 (85.90%) aligned 0 times 784s 8 (10.26%) aligned exactly 1 time 784s 3 (3.85%) aligned >1 times 784s 14.10% overall alignment rate 784s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.px.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.px.als.sorted 784s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.qJbFQMAC.debug.als | grep -v '^@PG' > /tmp/Sim.pm.qJbFQMAC.debug.als.sorted 784s diff -uw /tmp/Sim.pm.qJbFQMAC.debug.als.sorted /tmp/Sim.pm.qJbFQMAC.px.als.sorted 784s Flattened IUPAC characters 784s Mutating sequence Sim.pm.1 784s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutating sequence Sim.pm.2 784s Introducing 13 SNPs, 0/3 ref/read gaps, and 1 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutated reference genome to subject genome 784s SNPs introduced: 18 784s Reference gaps introduced: 0 784s Read gaps introduced: 4 784s Rearrangements introduced: 1 784s Created read sampler 784s Sampling 25 reads 784s Dumping reads to temporary files /tmp/Sim.pm.qJbFQMAC_1.fastq & /tmp/Sim.pm.qJbFQMAC_2.fastq 784s Parsing FASTA file /tmp/Sim.pm.qJbFQMAC.fa... 784s parsing sequence Sim.pm.1... 784s parsing sequence Sim.pm.2... 784s Parsed 76 reference bases 784s *** Run 100 of 100 784s /usr/bin/bowtie2 --large-index --cp-min 2 --np 2 --score-min L,5.72769412577804,7.99550871859223 --rdg 23.739554969064 --mm -M 19 --local --cp-ival 3 --trim3 7 -N 0 -L13 -q -x /tmp/Sim.pm.qJbFQMAC -1 /tmp/Sim.pm.qJbFQMAC_1.fastq -2 /tmp/Sim.pm.qJbFQMAC_2.fastq 784s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 784s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '3' because it was < 2 characters long 784s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '4' because it was < 2 characters long 784s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '5' because it was < 2 characters long 784s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '7' because it was < 2 characters long 784s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '17' because it was < 2 characters long 784s 25 reads; of these: 784s 19 (76.00%) were paired; of these: 784s 19 (100.00%) aligned concordantly 0 times 784s 0 (0.00%) aligned concordantly exactly 1 time 784s 0 (0.00%) aligned concordantly >1 times 784s ---- 784s 19 pairs aligned concordantly 0 times; of these: 784s 0 (0.00%) aligned discordantly 1 time 784s ---- 784s 19 pairs aligned 0 times concordantly or discordantly; of these: 784s 38 mates make up the pairs; of these: 784s 38 (100.00%) aligned 0 times 784s 0 (0.00%) aligned exactly 1 time 784s 0 (0.00%) aligned >1 times 784s 6 (24.00%) were unpaired; of these: 784s 6 (100.00%) aligned 0 times 784s 0 (0.00%) aligned exactly 1 time 784s 0 (0.00%) aligned >1 times 784s 0.00% overall alignment rate 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s --- Summary --- 784s Read 1 reference strings 784s Checked 0 alignments, 0 edits 784s --------------- 784s PASSED 784s PASSED 785s SUCCESS: help message was detected! 789s autopkgtest [14:29:10]: test run-unit-test: -----------------------] 791s autopkgtest [14:29:12]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 791s run-unit-test PASS 792s autopkgtest [14:29:13]: @@@@@@@@@@@@@@@@@@@@ summary 792s run-unit-test PASS 806s Creating nova instance adt-noble-ppc64el-bowtie2-20240312-141601-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240310.img (UUID 5ea2d65c-5c5d-423a-92f4-d5776b4c67ad)...